gromacs →
2021.3-4 →
armhf → 2021-10-26 18:49:56
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| gromacs 2021.3-4 (armhf) Tue, 26 Oct 2021 08:08:30 +0000 |
+==============================================================================+
Package: gromacs
Version: 2021.3-4
Source Version: 2021.3-4
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-816283cf-9b1a-415c-bb32-0ec987687141' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.5 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.9 MB in 29s (883 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'gromacs' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/debichem-team/gromacs.git
Please use:
git clone https://salsa.debian.org/debichem-team/gromacs.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 86.5 MB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main gromacs 2021.3-4 (dsc) [2985 B]
Get:2 http://172.17.0.1/private bookworm-staging/main gromacs 2021.3-4 (tar) [48.5 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main gromacs 2021.3-4 (tar) [38.0 MB]
Get:4 http://172.17.0.1/private bookworm-staging/main gromacs 2021.3-4 (diff) [40.5 kB]
Fetched 86.5 MB in 34s (2515 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/gromacs-iBBSHb/gromacs-2021.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gromacs-iBBSHb' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-aGvrju/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-aGvrju/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-aGvrju/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-aGvrju/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-aGvrju/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-aGvrju/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-aGvrju/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-aGvrju/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2787 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 42 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-aGvrju/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (22.4 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12484 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: chrpath, cmake (>= 3.13), debhelper-compat (= 13), libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libx11-dev, lsb-release, mpi-default-bin, mpi-default-dev, zlib1g-dev
Filtered Build-Depends: chrpath, cmake (>= 3.13), debhelper-compat (= 13), libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libx11-dev, lsb-release, mpi-default-bin, mpi-default-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-gromacs-dummy' in '/<<BUILDDIR>>/resolver-aGvrju/apt_archive/sbuild-build-depends-gromacs-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-gromacs-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-aGvrju/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-aGvrju/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-aGvrju/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-aGvrju/apt_archive ./ Sources [570 B]
Get:5 copy:/<<BUILDDIR>>/resolver-aGvrju/apt_archive ./ Packages [655 B]
Fetched 2558 B in 1s (3281 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install gromacs build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils chrpath cmake
cmake-data cpp-10 debhelper dh-autoreconf dh-elpa-helper
dh-strip-nondeterminism distro-info-data dwz emacsen-common file g++-10
gcc-10 gcc-10-base gcc-11-base gettext gettext-base gfortran-10 groff-base
ibverbs-providers intltool-debian libarchive-zip-perl libarchive13 libasan6
libatomic1 libblas-dev libblas3 libboost-dev libboost1.74-dev libbrotli1
libbsd0 libcbor0 libcc1-0 libcurl4 libdebhelper-perl libedit2 libelf1
libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7
libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1 libffi8
libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-single3 libfido2-1
libfile-stripnondeterminism-perl libgcc-10-dev libgcc-s1 libgfortran-10-dev
libgfortran5 libgomp1 libhwloc-dev libhwloc-plugins libhwloc15
libibverbs-dev libibverbs1 libicu67 libjs-jquery libjs-jquery-ui
libjsoncpp24 liblapack-dev liblapack3 libltdl-dev libltdl7 libmagic-mgc
libmagic1 libmd0 libmpdec3 libncurses6 libnghttp2-14 libnl-3-200 libnl-3-dev
libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev
libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev libpmix2 libprocps8
libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.9-minimal
libpython3.9-stdlib librdmacm1 librhash0 librtmp1 libsigsegv2 libssh2-1
libstdc++-10-dev libstdc++6 libsub-override-perl libtool libubsan1
libuchardet0 libuv1 libx11-6 libx11-data libx11-dev libxau-dev libxau6
libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext6 libxml2 libxnvctrl0
lsb-release m4 man-db media-types mpi-default-bin mpi-default-dev
ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf
procps python3 python3-minimal python3.9 python3.9-minimal sensible-utils
x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build
gcc-10-locales dh-make gcc-10-doc gettext-doc libasprintf-dev
libgettextpo-dev gfortran-10-doc libcoarrays-dev groff lrzip liblapack-doc
libboost-doc libboost1.74-doc libboost-atomic1.74-dev
libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev
libboost-contract1.74-dev libboost-coroutine1.74-dev
libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev
libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev
libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev
libboost-program-options1.74-dev libboost-python1.74-dev
libboost-random1.74-dev libboost-regex1.74-dev
libboost-serialization1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
libfftw3-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils
libstdc++-10-doc gcj-jdk libx11-doc libxcb-doc m4-doc apparmor less
www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh
monkeysphere ssh-askpass libmail-box-perl python3-doc python3-tk
python3-venv python3.9-venv python3.9-doc binfmt-support
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl javascript-common
libgpm2 libcoarrays-openmpi-dev publicsuffix xauth libmail-sendmail-perl
psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils chrpath cmake
cmake-data debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism
distro-info-data dwz emacsen-common file gettext gettext-base gfortran-10
groff-base ibverbs-providers intltool-debian libarchive-zip-perl
libarchive13 libblas-dev libblas3 libboost-dev libboost1.74-dev libbrotli1
libbsd0 libcbor0 libcurl4 libdebhelper-perl libedit2 libelf1 libevent-2.1-7
libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
libevent-pthreads-2.1-7 libexpat1 libfabric1 libffi8 libfftw3-bin
libfftw3-dev libfftw3-double3 libfftw3-single3 libfido2-1
libfile-stripnondeterminism-perl libgfortran-10-dev libgfortran5
libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu67
libjs-jquery libjs-jquery-ui libjsoncpp24 liblapack-dev liblapack3
libltdl-dev libltdl7 libmagic-mgc libmagic1 libmd0 libmpdec3 libncurses6
libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev
libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1
libpmix-dev libpmix2 libprocps8 libpsl5 libpthread-stubs0-dev
libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librdmacm1
librhash0 librtmp1 libsigsegv2 libssh2-1 libsub-override-perl libtool
libuchardet0 libuv1 libx11-6 libx11-data libx11-dev libxau-dev libxau6
libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext6 libxml2 libxnvctrl0
lsb-release m4 man-db media-types mpi-default-bin mpi-default-dev
ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf
procps python3 python3-minimal python3.9 python3.9-minimal
sbuild-build-depends-gromacs-dummy sensible-utils x11proto-dev
xorg-sgml-doctools xtrans-dev zlib1g-dev
The following packages will be upgraded:
cpp-10 g++-10 gcc-10 gcc-10-base gcc-11-base libasan6 libatomic1 libcc1-0
libgcc-10-dev libgcc-s1 libgomp1 libstdc++-10-dev libstdc++6 libubsan1
14 upgraded, 132 newly installed, 0 to remove and 28 not upgraded.
Need to get 99.6 MB of archives.
After this operation, 362 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-aGvrju/apt_archive ./ sbuild-build-depends-gromacs-dummy 0.invalid.0 [944 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-4 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libasan6 armhf 11.2.0-9+rpi1 [1947 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf libubsan1 armhf 11.2.0-9+rpi1 [798 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libgomp1 armhf 11.2.0-9+rpi1 [88.0 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf gcc-11-base armhf 11.2.0-9+rpi1 [206 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf libgcc-s1 armhf 11.2.0-9+rpi1 [36.2 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libcc1-0 armhf 11.2.0-9+rpi1 [38.0 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libatomic1 armhf 11.2.0-9+rpi1 [8184 B]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf libstdc++6 armhf 11.2.0-9+rpi1 [466 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-minimal armhf 3.9.7-4+rpi1 [794 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.1-2 [80.3 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf python3.9-minimal armhf 3.9.7-4+rpi1 [1632 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf media-types all 4.0.0 [30.3 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf libffi8 armhf 3.4.2-3 [21.3 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-stdlib armhf 3.9.7-4+rpi1 [1618 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf python3.9 armhf 3.9.7-4+rpi1 [480 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf python3 armhf 3.9.2-3 [37.9 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf g++-10 armhf 10.3.0-11+rpi1 [7350 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf gcc-10 armhf 10.3.0-11+rpi1 [13.4 MB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libstdc++-10-dev armhf 10.3.0-11+rpi1 [1755 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf libgcc-10-dev armhf 10.3.0-11+rpi1 [678 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf cpp-10 armhf 10.3.0-11+rpi1 [6690 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf gcc-10-base armhf 10.3.0-11+rpi1 [206 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf libncurses6 armhf 6.2+20201114-4 [79.7 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-5 [60.5 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-5 [475 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-1 [28.9 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.3-1 [103 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20210910-1 [81.2 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libcbor0 armhf 0.5.0+dfsg-2 [19.5 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf libfido2-1 armhf 1.8.0-1 [55.9 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf openssh-client armhf 1:8.4p1-6 [794 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.5-1 [823 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf libarchive13 armhf 3.4.3-2 [294 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:60 http://172.17.0.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-2 [161 kB]
Get:61 http://172.17.0.1/private bookworm-staging/main armhf libcurl4 armhf 7.74.0-1.3 [305 kB]
Get:62 http://172.17.0.1/private bookworm-staging/main armhf libjsoncpp24 armhf 1.9.4-5 [67.4 kB]
Get:63 http://172.17.0.1/private bookworm-staging/main armhf librhash0 armhf 1.4.2-1 [141 kB]
Get:64 http://172.17.0.1/private bookworm-staging/main armhf libuv1 armhf 1.42.0-1 [121 kB]
Get:65 http://172.17.0.1/private bookworm-staging/main armhf dh-elpa-helper all 2.0.9 [11.2 kB]
Get:66 http://172.17.0.1/private bookworm-staging/main armhf emacsen-common all 3.0.4 [19.3 kB]
Get:67 http://172.17.0.1/private bookworm-staging/main armhf cmake-data all 3.21.3-5 [1878 kB]
Get:68 http://172.17.0.1/private bookworm-staging/main armhf cmake armhf 3.21.3-5 [3470 kB]
Get:69 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:70 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:71 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:72 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:73 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:74 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-2 [26.3 kB]
Get:75 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-2 [15.5 kB]
Get:76 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:77 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:78 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:79 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:80 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:81 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:82 http://172.17.0.1/private bookworm-staging/main armhf distro-info-data all 0.52 [7596 B]
Get:83 http://172.17.0.1/private bookworm-staging/main armhf libgfortran5 armhf 11.2.0-9+rpi1 [235 kB]
Get:84 http://172.17.0.1/private bookworm-staging/main armhf libgfortran-10-dev armhf 10.3.0-11+rpi1 [277 kB]
Get:85 http://172.17.0.1/private bookworm-staging/main armhf gfortran-10 armhf 10.3.0-11+rpi1 [7201 kB]
Get:86 http://172.17.0.1/private bookworm-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:87 http://172.17.0.1/private bookworm-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:88 http://172.17.0.1/private bookworm-staging/main armhf libibverbs1 armhf 36.0-1 [53.2 kB]
Get:89 http://172.17.0.1/private bookworm-staging/main armhf ibverbs-providers armhf 36.0-1 [27.3 kB]
Get:90 http://172.17.0.1/private bookworm-staging/main armhf libblas3 armhf 3.10.0-1 [108 kB]
Get:91 http://172.17.0.1/private bookworm-staging/main armhf libblas-dev armhf 3.10.0-1 [113 kB]
Get:92 http://172.17.0.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-9 [9534 kB]
Get:93 http://172.17.0.1/private bookworm-staging/main armhf libboost-dev armhf 1.74.0.3+b1 [4820 B]
Get:94 http://172.17.0.1/private bookworm-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-1 [167 kB]
Get:95 http://172.17.0.1/private bookworm-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-1 [126 kB]
Get:96 http://172.17.0.1/private bookworm-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-1 [100 kB]
Get:97 http://172.17.0.1/private bookworm-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-1 [56.8 kB]
Get:98 http://172.17.0.1/private bookworm-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-1 [61.7 kB]
Get:99 http://172.17.0.1/private bookworm-staging/main armhf libevent-dev armhf 2.1.12-stable-1 [281 kB]
Get:100 http://172.17.0.1/private bookworm-staging/main armhf librdmacm1 armhf 36.0-1 [60.1 kB]
Get:101 http://172.17.0.1/private bookworm-staging/main armhf libfabric1 armhf 1.11.0-2 [311 kB]
Get:102 http://172.17.0.1/private bookworm-staging/main armhf libfftw3-double3 armhf 3.3.8-2 [429 kB]
Get:103 http://172.17.0.1/private bookworm-staging/main armhf libfftw3-single3 armhf 3.3.8-2 [633 kB]
Get:104 http://172.17.0.1/private bookworm-staging/main armhf libfftw3-bin armhf 3.3.8-2 [43.6 kB]
Get:105 http://172.17.0.1/private bookworm-staging/main armhf libfftw3-dev armhf 3.3.8-2 [1060 kB]
Get:106 http://172.17.0.1/private bookworm-staging/main armhf libhwloc15 armhf 2.5.0+dfsg-2 [126 kB]
Get:107 http://172.17.0.1/private bookworm-staging/main armhf libnuma1 armhf 2.0.14-3 [21.8 kB]
Get:108 http://172.17.0.1/private bookworm-staging/main armhf libnuma-dev armhf 2.0.14-3 [34.7 kB]
Get:109 http://172.17.0.1/private bookworm-staging/main armhf libltdl7 armhf 2.4.6-15 [388 kB]
Get:110 http://172.17.0.1/private bookworm-staging/main armhf libltdl-dev armhf 2.4.6-15 [159 kB]
Get:111 http://172.17.0.1/private bookworm-staging/main armhf libhwloc-dev armhf 2.5.0+dfsg-2 [197 kB]
Get:112 http://172.17.0.1/private bookworm-staging/main armhf libpciaccess0 armhf 0.16-1 [51.0 kB]
Get:113 http://172.17.0.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:114 http://172.17.0.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:115 http://172.17.0.1/private bookworm-staging/main armhf libxcb1 armhf 1.14-3 [136 kB]
Get:116 http://172.17.0.1/private bookworm-staging/main armhf libx11-data all 2:1.7.2-2 [311 kB]
Get:117 http://172.17.0.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.7.2-2 [704 kB]
Get:118 http://172.17.0.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:119 http://172.17.0.1/private bookworm-staging/main armhf libxnvctrl0 armhf 470.57.02-2 [26.0 kB]
Get:120 http://172.17.0.1/private bookworm-staging/main armhf ocl-icd-libopencl1 armhf 2.2.14-3 [39.9 kB]
Get:121 http://172.17.0.1/private bookworm-staging/main armhf libhwloc-plugins armhf 2.5.0+dfsg-2 [20.0 kB]
Get:122 http://172.17.0.1/private bookworm-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:123 http://172.17.0.1/private bookworm-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:124 http://172.17.0.1/private bookworm-staging/main armhf libibverbs-dev armhf 36.0-1 [186 kB]
Get:125 http://172.17.0.1/private bookworm-staging/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB]
Get:126 http://172.17.0.1/private bookworm-staging/main armhf libjs-jquery-ui all 1.12.1+dfsg-8 [232 kB]
Get:127 http://172.17.0.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.0-1 [1594 kB]
Get:128 http://172.17.0.1/private bookworm-staging/main armhf liblapack-dev armhf 3.10.0-1 [2872 kB]
Get:129 http://172.17.0.1/private bookworm-staging/main armhf libpmix2 armhf 4.1.1~rc4-1 [477 kB]
Get:130 http://172.17.0.1/private bookworm-staging/main armhf libopenmpi3 armhf 4.1.2~rc1-4+rpi1 [1779 kB]
Get:131 http://172.17.0.1/private bookworm-staging/main armhf openmpi-common all 4.1.2~rc1-4+rpi1 [180 kB]
Get:132 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:133 http://172.17.0.1/private bookworm-staging/main armhf libpmix-dev armhf 4.1.1~rc4-1 [638 kB]
Get:134 http://172.17.0.1/private bookworm-staging/main armhf openmpi-bin armhf 4.1.2~rc1-4+rpi1 [209 kB]
Get:135 http://172.17.0.1/private bookworm-staging/main armhf libopenmpi-dev armhf 4.1.2~rc1-4+rpi1 [937 kB]
Get:136 http://172.17.0.1/private bookworm-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:137 http://172.17.0.1/private bookworm-staging/main armhf xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get:138 http://172.17.0.1/private bookworm-staging/main armhf x11proto-dev all 2021.5-1 [599 kB]
Get:139 http://172.17.0.1/private bookworm-staging/main armhf libxau-dev armhf 1:1.0.9-1 [22.3 kB]
Get:140 http://172.17.0.1/private bookworm-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:141 http://172.17.0.1/private bookworm-staging/main armhf xtrans-dev all 1.4.0-1 [98.7 kB]
Get:142 http://172.17.0.1/private bookworm-staging/main armhf libxcb1-dev armhf 1.14-3 [171 kB]
Get:143 http://172.17.0.1/private bookworm-staging/main armhf libx11-dev armhf 2:1.7.2-2 [780 kB]
Get:144 http://172.17.0.1/private bookworm-staging/main armhf lsb-release all 11.1.0+rpi1 [28.1 kB]
Get:145 http://172.17.0.1/private bookworm-staging/main armhf mpi-default-bin armhf 1.14 [4752 B]
Get:146 http://172.17.0.1/private bookworm-staging/main armhf mpi-default-dev armhf 1.14 [5548 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 99.6 MB in 37s (2696 kB/s)
Selecting previously unselected package bsdextrautils.
(Reading database ... 12484 files and directories currently installed.)
Preparing to unpack .../bsdextrautils_2.37.2-4_armhf.deb ...
Unpacking bsdextrautils (2.37.2-4) ...
Preparing to unpack .../libasan6_11.2.0-9+rpi1_armhf.deb ...
Unpacking libasan6:armhf (11.2.0-9+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libubsan1_11.2.0-9+rpi1_armhf.deb ...
Unpacking libubsan1:armhf (11.2.0-9+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libgomp1_11.2.0-9+rpi1_armhf.deb ...
Unpacking libgomp1:armhf (11.2.0-9+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../gcc-11-base_11.2.0-9+rpi1_armhf.deb ...
Unpacking gcc-11-base:armhf (11.2.0-9+rpi1) over (11.2.0-4+rpi1) ...
Setting up gcc-11-base:armhf (11.2.0-9+rpi1) ...
(Reading database ... 12515 files and directories currently installed.)
Preparing to unpack .../libgcc-s1_11.2.0-9+rpi1_armhf.deb ...
Unpacking libgcc-s1:armhf (11.2.0-9+rpi1) over (11.2.0-4+rpi1) ...
Setting up libgcc-s1:armhf (11.2.0-9+rpi1) ...
(Reading database ... 12515 files and directories currently installed.)
Preparing to unpack .../libcc1-0_11.2.0-9+rpi1_armhf.deb ...
Unpacking libcc1-0:armhf (11.2.0-9+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libatomic1_11.2.0-9+rpi1_armhf.deb ...
Unpacking libatomic1:armhf (11.2.0-9+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libstdc++6_11.2.0-9+rpi1_armhf.deb ...
Unpacking libstdc++6:armhf (11.2.0-9+rpi1) over (11.2.0-4+rpi1) ...
Setting up libstdc++6:armhf (11.2.0-9+rpi1) ...
Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 12515 files and directories currently installed.)
Preparing to unpack .../0-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../1-groff-base_1.22.4-7_armhf.deb ...
Unpacking groff-base (1.22.4-7) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../2-libpipeline1_1.5.3-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.3-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../3-man-db_2.9.4-2_armhf.deb ...
Unpacking man-db (2.9.4-2) ...
Selecting previously unselected package libpython3.9-minimal:armhf.
Preparing to unpack .../4-libpython3.9-minimal_3.9.7-4+rpi1_armhf.deb ...
Unpacking libpython3.9-minimal:armhf (3.9.7-4+rpi1) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../5-libexpat1_2.4.1-2_armhf.deb ...
Unpacking libexpat1:armhf (2.4.1-2) ...
Selecting previously unselected package python3.9-minimal.
Preparing to unpack .../6-python3.9-minimal_3.9.7-4+rpi1_armhf.deb ...
Unpacking python3.9-minimal (3.9.7-4+rpi1) ...
Setting up libpython3.9-minimal:armhf (3.9.7-4+rpi1) ...
Setting up libexpat1:armhf (2.4.1-2) ...
Setting up python3.9-minimal (3.9.7-4+rpi1) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 13351 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.9.2-3_armhf.deb ...
Unpacking python3-minimal (3.9.2-3) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_4.0.0_all.deb ...
Unpacking media-types (4.0.0) ...
Selecting previously unselected package libffi8:armhf.
Preparing to unpack .../2-libffi8_3.4.2-3_armhf.deb ...
Unpacking libffi8:armhf (3.4.2-3) ...
Selecting previously unselected package libmpdec3:armhf.
Preparing to unpack .../3-libmpdec3_2.5.1-2+rpi1_armhf.deb ...
Unpacking libmpdec3:armhf (2.5.1-2+rpi1) ...
Selecting previously unselected package libpython3.9-stdlib:armhf.
Preparing to unpack .../4-libpython3.9-stdlib_3.9.7-4+rpi1_armhf.deb ...
Unpacking libpython3.9-stdlib:armhf (3.9.7-4+rpi1) ...
Selecting previously unselected package python3.9.
Preparing to unpack .../5-python3.9_3.9.7-4+rpi1_armhf.deb ...
Unpacking python3.9 (3.9.7-4+rpi1) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../6-libpython3-stdlib_3.9.2-3_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.9.2-3) ...
Setting up python3-minimal (3.9.2-3) ...
Selecting previously unselected package python3.
(Reading database ... 13754 files and directories currently installed.)
Preparing to unpack .../000-python3_3.9.2-3_armhf.deb ...
Unpacking python3 (3.9.2-3) ...
Preparing to unpack .../001-g++-10_10.3.0-11+rpi1_armhf.deb ...
Unpacking g++-10 (10.3.0-11+rpi1) over (10.3.0-9+rpi1) ...
Preparing to unpack .../002-gcc-10_10.3.0-11+rpi1_armhf.deb ...
Unpacking gcc-10 (10.3.0-11+rpi1) over (10.3.0-9+rpi1) ...
Preparing to unpack .../003-libstdc++-10-dev_10.3.0-11+rpi1_armhf.deb ...
Unpacking libstdc++-10-dev:armhf (10.3.0-11+rpi1) over (10.3.0-9+rpi1) ...
Preparing to unpack .../004-libgcc-10-dev_10.3.0-11+rpi1_armhf.deb ...
Unpacking libgcc-10-dev:armhf (10.3.0-11+rpi1) over (10.3.0-9+rpi1) ...
Preparing to unpack .../005-cpp-10_10.3.0-11+rpi1_armhf.deb ...
Unpacking cpp-10 (10.3.0-11+rpi1) over (10.3.0-9+rpi1) ...
Preparing to unpack .../006-gcc-10-base_10.3.0-11+rpi1_armhf.deb ...
Unpacking gcc-10-base:armhf (10.3.0-11+rpi1) over (10.3.0-9+rpi1) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../007-libncurses6_6.2+20201114-4_armhf.deb ...
Unpacking libncurses6:armhf (6.2+20201114-4) ...
Selecting previously unselected package libprocps8:armhf.
Preparing to unpack .../008-libprocps8_2%3a3.3.17-5_armhf.deb ...
Unpacking libprocps8:armhf (2:3.3.17-5) ...
Selecting previously unselected package procps.
Preparing to unpack .../009-procps_2%3a3.3.17-5_armhf.deb ...
Unpacking procps (2:3.3.17-5) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../010-sensible-utils_0.0.17_all.deb ...
Unpacking sensible-utils (0.0.17) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../011-libmagic-mgc_1%3a5.39-3_armhf.deb ...
Unpacking libmagic-mgc (1:5.39-3) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../012-libmagic1_1%3a5.39-3_armhf.deb ...
Unpacking libmagic1:armhf (1:5.39-3) ...
Selecting previously unselected package file.
Preparing to unpack .../013-file_1%3a5.39-3_armhf.deb ...
Unpacking file (1:5.39-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../014-gettext-base_0.21-4_armhf.deb ...
Unpacking gettext-base (0.21-4) ...
Selecting previously unselected package libmd0:armhf.
Preparing to unpack .../015-libmd0_1.0.4-1_armhf.deb ...
Unpacking libmd0:armhf (1.0.4-1) ...
Selecting previously unselected package libbsd0:armhf.
Preparing to unpack .../016-libbsd0_0.11.3-1_armhf.deb ...
Unpacking libbsd0:armhf (0.11.3-1) ...
Selecting previously unselected package libedit2:armhf.
Preparing to unpack .../017-libedit2_3.1-20210910-1_armhf.deb ...
Unpacking libedit2:armhf (3.1-20210910-1) ...
Selecting previously unselected package libcbor0:armhf.
Preparing to unpack .../018-libcbor0_0.5.0+dfsg-2_armhf.deb ...
Unpacking libcbor0:armhf (0.5.0+dfsg-2) ...
Selecting previously unselected package libfido2-1:armhf.
Preparing to unpack .../019-libfido2-1_1.8.0-1_armhf.deb ...
Unpacking libfido2-1:armhf (1.8.0-1) ...
Selecting previously unselected package openssh-client.
Preparing to unpack .../020-openssh-client_1%3a8.4p1-6_armhf.deb ...
Unpacking openssh-client (1:8.4p1-6) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../021-libsigsegv2_2.13-1_armhf.deb ...
Unpacking libsigsegv2:armhf (2.13-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../022-m4_1.4.18-5_armhf.deb ...
Unpacking m4 (1.4.18-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../023-autoconf_2.71-2_all.deb ...
Unpacking autoconf (2.71-2) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../024-autotools-dev_20180224.1+nmu1_all.deb ...
Unpacking autotools-dev (20180224.1+nmu1) ...
Selecting previously unselected package automake.
Preparing to unpack .../025-automake_1%3a1.16.5-1_all.deb ...
Unpacking automake (1:1.16.5-1) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../026-autopoint_0.21-4_all.deb ...
Unpacking autopoint (0.21-4) ...
Selecting previously unselected package chrpath.
Preparing to unpack .../027-chrpath_0.16-2_armhf.deb ...
Unpacking chrpath (0.16-2) ...
Selecting previously unselected package libicu67:armhf.
Preparing to unpack .../028-libicu67_67.1-7_armhf.deb ...
Unpacking libicu67:armhf (67.1-7) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../029-libxml2_2.9.12+dfsg-5_armhf.deb ...
Unpacking libxml2:armhf (2.9.12+dfsg-5) ...
Selecting previously unselected package libarchive13:armhf.
Preparing to unpack .../030-libarchive13_3.4.3-2_armhf.deb ...
Unpacking libarchive13:armhf (3.4.3-2) ...
Selecting previously unselected package libbrotli1:armhf.
Preparing to unpack .../031-libbrotli1_1.0.9-2+b1_armhf.deb ...
Unpacking libbrotli1:armhf (1.0.9-2+b1) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../032-libnghttp2-14_1.43.0-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.43.0-1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../033-libpsl5_0.21.0-1.2_armhf.deb ...
Unpacking libpsl5:armhf (0.21.0-1.2) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../034-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../035-libssh2-1_1.10.0-2_armhf.deb ...
Unpacking libssh2-1:armhf (1.10.0-2) ...
Selecting previously unselected package libcurl4:armhf.
Preparing to unpack .../036-libcurl4_7.74.0-1.3_armhf.deb ...
Unpacking libcurl4:armhf (7.74.0-1.3) ...
Selecting previously unselected package libjsoncpp24:armhf.
Preparing to unpack .../037-libjsoncpp24_1.9.4-5_armhf.deb ...
Unpacking libjsoncpp24:armhf (1.9.4-5) ...
Selecting previously unselected package librhash0:armhf.
Preparing to unpack .../038-librhash0_1.4.2-1_armhf.deb ...
Unpacking librhash0:armhf (1.4.2-1) ...
Selecting previously unselected package libuv1:armhf.
Preparing to unpack .../039-libuv1_1.42.0-1_armhf.deb ...
Unpacking libuv1:armhf (1.42.0-1) ...
Selecting previously unselected package dh-elpa-helper.
Preparing to unpack .../040-dh-elpa-helper_2.0.9_all.deb ...
Unpacking dh-elpa-helper (2.0.9) ...
Selecting previously unselected package emacsen-common.
Preparing to unpack .../041-emacsen-common_3.0.4_all.deb ...
Unpacking emacsen-common (3.0.4) ...
Selecting previously unselected package cmake-data.
Preparing to unpack .../042-cmake-data_3.21.3-5_all.deb ...
Unpacking cmake-data (3.21.3-5) ...
Selecting previously unselected package cmake.
Preparing to unpack .../043-cmake_3.21.3-5_armhf.deb ...
Unpacking cmake (3.21.3-5) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../044-libdebhelper-perl_13.5.2_all.deb ...
Unpacking libdebhelper-perl (13.5.2) ...
Selecting previously unselected package libtool.
Preparing to unpack .../045-libtool_2.4.6-15_all.deb ...
Unpacking libtool (2.4.6-15) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../046-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../047-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../048-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../049-libfile-stripnondeterminism-perl_1.12.0-2_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.12.0-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../050-dh-strip-nondeterminism_1.12.0-2_all.deb ...
Unpacking dh-strip-nondeterminism (1.12.0-2) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../051-libelf1_0.185-2_armhf.deb ...
Unpacking libelf1:armhf (0.185-2) ...
Selecting previously unselected package dwz.
Preparing to unpack .../052-dwz_0.14-1_armhf.deb ...
Unpacking dwz (0.14-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../053-gettext_0.21-4_armhf.deb ...
Unpacking gettext (0.21-4) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../054-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../055-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../056-debhelper_13.5.2_all.deb ...
Unpacking debhelper (13.5.2) ...
Selecting previously unselected package distro-info-data.
Preparing to unpack .../057-distro-info-data_0.52_all.deb ...
Unpacking distro-info-data (0.52) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../058-libgfortran5_11.2.0-9+rpi1_armhf.deb ...
Unpacking libgfortran5:armhf (11.2.0-9+rpi1) ...
Selecting previously unselected package libgfortran-10-dev:armhf.
Preparing to unpack .../059-libgfortran-10-dev_10.3.0-11+rpi1_armhf.deb ...
Unpacking libgfortran-10-dev:armhf (10.3.0-11+rpi1) ...
Selecting previously unselected package gfortran-10.
Preparing to unpack .../060-gfortran-10_10.3.0-11+rpi1_armhf.deb ...
Unpacking gfortran-10 (10.3.0-11+rpi1) ...
Selecting previously unselected package libnl-3-200:armhf.
Preparing to unpack .../061-libnl-3-200_3.4.0-1_armhf.deb ...
Unpacking libnl-3-200:armhf (3.4.0-1) ...
Selecting previously unselected package libnl-route-3-200:armhf.
Preparing to unpack .../062-libnl-route-3-200_3.4.0-1_armhf.deb ...
Unpacking libnl-route-3-200:armhf (3.4.0-1) ...
Selecting previously unselected package libibverbs1:armhf.
Preparing to unpack .../063-libibverbs1_36.0-1_armhf.deb ...
Unpacking libibverbs1:armhf (36.0-1) ...
Selecting previously unselected package ibverbs-providers:armhf.
Preparing to unpack .../064-ibverbs-providers_36.0-1_armhf.deb ...
Unpacking ibverbs-providers:armhf (36.0-1) ...
Selecting previously unselected package libblas3:armhf.
Preparing to unpack .../065-libblas3_3.10.0-1_armhf.deb ...
Unpacking libblas3:armhf (3.10.0-1) ...
Selecting previously unselected package libblas-dev:armhf.
Preparing to unpack .../066-libblas-dev_3.10.0-1_armhf.deb ...
Unpacking libblas-dev:armhf (3.10.0-1) ...
Selecting previously unselected package libboost1.74-dev:armhf.
Preparing to unpack .../067-libboost1.74-dev_1.74.0-9_armhf.deb ...
Unpacking libboost1.74-dev:armhf (1.74.0-9) ...
Selecting previously unselected package libboost-dev:armhf.
Preparing to unpack .../068-libboost-dev_1.74.0.3+b1_armhf.deb ...
Unpacking libboost-dev:armhf (1.74.0.3+b1) ...
Selecting previously unselected package libevent-2.1-7:armhf.
Preparing to unpack .../069-libevent-2.1-7_2.1.12-stable-1_armhf.deb ...
Unpacking libevent-2.1-7:armhf (2.1.12-stable-1) ...
Selecting previously unselected package libevent-core-2.1-7:armhf.
Preparing to unpack .../070-libevent-core-2.1-7_2.1.12-stable-1_armhf.deb ...
Unpacking libevent-core-2.1-7:armhf (2.1.12-stable-1) ...
Selecting previously unselected package libevent-extra-2.1-7:armhf.
Preparing to unpack .../071-libevent-extra-2.1-7_2.1.12-stable-1_armhf.deb ...
Unpacking libevent-extra-2.1-7:armhf (2.1.12-stable-1) ...
Selecting previously unselected package libevent-pthreads-2.1-7:armhf.
Preparing to unpack .../072-libevent-pthreads-2.1-7_2.1.12-stable-1_armhf.deb ...
Unpacking libevent-pthreads-2.1-7:armhf (2.1.12-stable-1) ...
Selecting previously unselected package libevent-openssl-2.1-7:armhf.
Preparing to unpack .../073-libevent-openssl-2.1-7_2.1.12-stable-1_armhf.deb ...
Unpacking libevent-openssl-2.1-7:armhf (2.1.12-stable-1) ...
Selecting previously unselected package libevent-dev.
Preparing to unpack .../074-libevent-dev_2.1.12-stable-1_armhf.deb ...
Unpacking libevent-dev (2.1.12-stable-1) ...
Selecting previously unselected package librdmacm1:armhf.
Preparing to unpack .../075-librdmacm1_36.0-1_armhf.deb ...
Unpacking librdmacm1:armhf (36.0-1) ...
Selecting previously unselected package libfabric1.
Preparing to unpack .../076-libfabric1_1.11.0-2_armhf.deb ...
Unpacking libfabric1 (1.11.0-2) ...
Selecting previously unselected package libfftw3-double3:armhf.
Preparing to unpack .../077-libfftw3-double3_3.3.8-2_armhf.deb ...
Unpacking libfftw3-double3:armhf (3.3.8-2) ...
Selecting previously unselected package libfftw3-single3:armhf.
Preparing to unpack .../078-libfftw3-single3_3.3.8-2_armhf.deb ...
Unpacking libfftw3-single3:armhf (3.3.8-2) ...
Selecting previously unselected package libfftw3-bin.
Preparing to unpack .../079-libfftw3-bin_3.3.8-2_armhf.deb ...
Unpacking libfftw3-bin (3.3.8-2) ...
Selecting previously unselected package libfftw3-dev:armhf.
Preparing to unpack .../080-libfftw3-dev_3.3.8-2_armhf.deb ...
Unpacking libfftw3-dev:armhf (3.3.8-2) ...
Selecting previously unselected package libhwloc15:armhf.
Preparing to unpack .../081-libhwloc15_2.5.0+dfsg-2_armhf.deb ...
Unpacking libhwloc15:armhf (2.5.0+dfsg-2) ...
Selecting previously unselected package libnuma1:armhf.
Preparing to unpack .../082-libnuma1_2.0.14-3_armhf.deb ...
Unpacking libnuma1:armhf (2.0.14-3) ...
Selecting previously unselected package libnuma-dev:armhf.
Preparing to unpack .../083-libnuma-dev_2.0.14-3_armhf.deb ...
Unpacking libnuma-dev:armhf (2.0.14-3) ...
Selecting previously unselected package libltdl7:armhf.
Preparing to unpack .../084-libltdl7_2.4.6-15_armhf.deb ...
Unpacking libltdl7:armhf (2.4.6-15) ...
Selecting previously unselected package libltdl-dev:armhf.
Preparing to unpack .../085-libltdl-dev_2.4.6-15_armhf.deb ...
Unpacking libltdl-dev:armhf (2.4.6-15) ...
Selecting previously unselected package libhwloc-dev:armhf.
Preparing to unpack .../086-libhwloc-dev_2.5.0+dfsg-2_armhf.deb ...
Unpacking libhwloc-dev:armhf (2.5.0+dfsg-2) ...
Selecting previously unselected package libpciaccess0:armhf.
Preparing to unpack .../087-libpciaccess0_0.16-1_armhf.deb ...
Unpacking libpciaccess0:armhf (0.16-1) ...
Selecting previously unselected package libxau6:armhf.
Preparing to unpack .../088-libxau6_1%3a1.0.9-1_armhf.deb ...
Unpacking libxau6:armhf (1:1.0.9-1) ...
Selecting previously unselected package libxdmcp6:armhf.
Preparing to unpack .../089-libxdmcp6_1%3a1.1.2-3_armhf.deb ...
Unpacking libxdmcp6:armhf (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:armhf.
Preparing to unpack .../090-libxcb1_1.14-3_armhf.deb ...
Unpacking libxcb1:armhf (1.14-3) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../091-libx11-data_2%3a1.7.2-2_all.deb ...
Unpacking libx11-data (2:1.7.2-2) ...
Selecting previously unselected package libx11-6:armhf.
Preparing to unpack .../092-libx11-6_2%3a1.7.2-2_armhf.deb ...
Unpacking libx11-6:armhf (2:1.7.2-2) ...
Selecting previously unselected package libxext6:armhf.
Preparing to unpack .../093-libxext6_2%3a1.3.4-1_armhf.deb ...
Unpacking libxext6:armhf (2:1.3.4-1) ...
Selecting previously unselected package libxnvctrl0:armhf.
Preparing to unpack .../094-libxnvctrl0_470.57.02-2_armhf.deb ...
Unpacking libxnvctrl0:armhf (470.57.02-2) ...
Selecting previously unselected package ocl-icd-libopencl1:armhf.
Preparing to unpack .../095-ocl-icd-libopencl1_2.2.14-3_armhf.deb ...
Unpacking ocl-icd-libopencl1:armhf (2.2.14-3) ...
Selecting previously unselected package libhwloc-plugins:armhf.
Preparing to unpack .../096-libhwloc-plugins_2.5.0+dfsg-2_armhf.deb ...
Unpacking libhwloc-plugins:armhf (2.5.0+dfsg-2) ...
Selecting previously unselected package libnl-3-dev:armhf.
Preparing to unpack .../097-libnl-3-dev_3.4.0-1_armhf.deb ...
Unpacking libnl-3-dev:armhf (3.4.0-1) ...
Selecting previously unselected package libnl-route-3-dev:armhf.
Preparing to unpack .../098-libnl-route-3-dev_3.4.0-1_armhf.deb ...
Unpacking libnl-route-3-dev:armhf (3.4.0-1) ...
Selecting previously unselected package libibverbs-dev:armhf.
Preparing to unpack .../099-libibverbs-dev_36.0-1_armhf.deb ...
Unpacking libibverbs-dev:armhf (36.0-1) ...
Selecting previously unselected package libjs-jquery.
Preparing to unpack .../100-libjs-jquery_3.5.1+dfsg+~3.5.5-7_all.deb ...
Unpacking libjs-jquery (3.5.1+dfsg+~3.5.5-7) ...
Selecting previously unselected package libjs-jquery-ui.
Preparing to unpack .../101-libjs-jquery-ui_1.12.1+dfsg-8_all.deb ...
Unpacking libjs-jquery-ui (1.12.1+dfsg-8) ...
Selecting previously unselected package liblapack3:armhf.
Preparing to unpack .../102-liblapack3_3.10.0-1_armhf.deb ...
Unpacking liblapack3:armhf (3.10.0-1) ...
Selecting previously unselected package liblapack-dev:armhf.
Preparing to unpack .../103-liblapack-dev_3.10.0-1_armhf.deb ...
Unpacking liblapack-dev:armhf (3.10.0-1) ...
Selecting previously unselected package libpmix2:armhf.
Preparing to unpack .../104-libpmix2_4.1.1~rc4-1_armhf.deb ...
Unpacking libpmix2:armhf (4.1.1~rc4-1) ...
Selecting previously unselected package libopenmpi3:armhf.
Preparing to unpack .../105-libopenmpi3_4.1.2~rc1-4+rpi1_armhf.deb ...
Unpacking libopenmpi3:armhf (4.1.2~rc1-4+rpi1) ...
Selecting previously unselected package openmpi-common.
Preparing to unpack .../106-openmpi-common_4.1.2~rc1-4+rpi1_all.deb ...
Unpacking openmpi-common (4.1.2~rc1-4+rpi1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../107-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Selecting previously unselected package libpmix-dev:armhf.
Preparing to unpack .../108-libpmix-dev_4.1.1~rc4-1_armhf.deb ...
Unpacking libpmix-dev:armhf (4.1.1~rc4-1) ...
Selecting previously unselected package openmpi-bin.
Preparing to unpack .../109-openmpi-bin_4.1.2~rc1-4+rpi1_armhf.deb ...
Unpacking openmpi-bin (4.1.2~rc1-4+rpi1) ...
Selecting previously unselected package libopenmpi-dev:armhf.
Preparing to unpack .../110-libopenmpi-dev_4.1.2~rc1-4+rpi1_armhf.deb ...
Unpacking libopenmpi-dev:armhf (4.1.2~rc1-4+rpi1) ...
Selecting previously unselected package libpthread-stubs0-dev:armhf.
Preparing to unpack .../111-libpthread-stubs0-dev_0.4-1_armhf.deb ...
Unpacking libpthread-stubs0-dev:armhf (0.4-1) ...
Selecting previously unselected package xorg-sgml-doctools.
Preparing to unpack .../112-xorg-sgml-doctools_1%3a1.11-1.1_all.deb ...
Unpacking xorg-sgml-doctools (1:1.11-1.1) ...
Selecting previously unselected package x11proto-dev.
Preparing to unpack .../113-x11proto-dev_2021.5-1_all.deb ...
Unpacking x11proto-dev (2021.5-1) ...
Selecting previously unselected package libxau-dev:armhf.
Preparing to unpack .../114-libxau-dev_1%3a1.0.9-1_armhf.deb ...
Unpacking libxau-dev:armhf (1:1.0.9-1) ...
Selecting previously unselected package libxdmcp-dev:armhf.
Preparing to unpack .../115-libxdmcp-dev_1%3a1.1.2-3_armhf.deb ...
Unpacking libxdmcp-dev:armhf (1:1.1.2-3) ...
Selecting previously unselected package xtrans-dev.
Preparing to unpack .../116-xtrans-dev_1.4.0-1_all.deb ...
Unpacking xtrans-dev (1.4.0-1) ...
Selecting previously unselected package libxcb1-dev:armhf.
Preparing to unpack .../117-libxcb1-dev_1.14-3_armhf.deb ...
Unpacking libxcb1-dev:armhf (1.14-3) ...
Selecting previously unselected package libx11-dev:armhf.
Preparing to unpack .../118-libx11-dev_2%3a1.7.2-2_armhf.deb ...
Unpacking libx11-dev:armhf (2:1.7.2-2) ...
Selecting previously unselected package lsb-release.
Preparing to unpack .../119-lsb-release_11.1.0+rpi1_all.deb ...
Unpacking lsb-release (11.1.0+rpi1) ...
Selecting previously unselected package mpi-default-bin.
Preparing to unpack .../120-mpi-default-bin_1.14_armhf.deb ...
Unpacking mpi-default-bin (1.14) ...
Selecting previously unselected package mpi-default-dev.
Preparing to unpack .../121-mpi-default-dev_1.14_armhf.deb ...
Unpacking mpi-default-dev (1.14) ...
Selecting previously unselected package sbuild-build-depends-gromacs-dummy.
Preparing to unpack .../122-sbuild-build-depends-gromacs-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-gromacs-dummy (0.invalid.0) ...
Setting up media-types (4.0.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libpciaccess0:armhf (0.16-1) ...
Setting up libxau6:armhf (1:1.0.9-1) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up bsdextrautils (2.37.2-4) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up distro-info-data (0.52) ...
Setting up libdebhelper-perl (13.5.2) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libcbor0:armhf (0.5.0+dfsg-2) ...
Setting up libnghttp2-14:armhf (1.43.0-1) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up libgomp1:armhf (11.2.0-9+rpi1) ...
Setting up libpthread-stubs0-dev:armhf (0.4-1) ...
Setting up libasan6:armhf (11.2.0-9+rpi1) ...
Setting up xtrans-dev (1.4.0-1) ...
Setting up gcc-10-base:armhf (10.3.0-11+rpi1) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libblas3:armhf (3.10.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libuv1:armhf (1.42.0-1) ...
Setting up emacsen-common (3.0.4) ...
Setting up libx11-data (2:1.7.2-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up dh-elpa-helper (2.0.9) ...
Setting up libncurses6:armhf (6.2+20201114-4) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up libhwloc15:armhf (2.5.0+dfsg-2) ...
Setting up libevent-core-2.1-7:armhf (2.1.12-stable-1) ...
Setting up libatomic1:armhf (11.2.0-9+rpi1) ...
Setting up libevent-2.1-7:armhf (2.1.12-stable-1) ...
Setting up autopoint (0.21-4) ...
Setting up libltdl7:armhf (2.4.6-15) ...
Setting up libfftw3-double3:armhf (3.3.8-2) ...
Setting up libgfortran5:armhf (11.2.0-9+rpi1) ...
Setting up libjsoncpp24:armhf (1.9.4-5) ...
Setting up libubsan1:armhf (11.2.0-9+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libffi8:armhf (3.4.2-3) ...
Setting up libnuma1:armhf (2.0.14-3) ...
Setting up libmd0:armhf (1.0.4-1) ...
Setting up sensible-utils (0.0.17) ...
Setting up ocl-icd-libopencl1:armhf (2.2.14-3) ...
Setting up librhash0:armhf (1.4.2-1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libnl-3-200:armhf (3.4.0-1) ...
Setting up libmpdec3:armhf (2.5.1-2+rpi1) ...
Setting up openmpi-common (4.1.2~rc1-4+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.10.0-2) ...
Setting up xorg-sgml-doctools (1:1.11-1.1) ...
Setting up cmake-data (3.21.3-5) ...
Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ...
Setting up libfido2-1:armhf (1.8.0-1) ...
Setting up libbsd0:armhf (0.11.3-1) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up libcc1-0:armhf (11.2.0-9+rpi1) ...
Setting up chrpath (0.16-2) ...
Setting up libprocps8:armhf (2:3.3.17-5) ...
Setting up cpp-10 (10.3.0-11+rpi1) ...
Setting up libblas-dev:armhf (3.10.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up libpython3.9-stdlib:armhf (3.9.7-4+rpi1) ...
Setting up libpython3-stdlib:armhf (3.9.2-3) ...
Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-1) ...
Setting up x11proto-dev (2021.5-1) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-2) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libevent-extra-2.1-7:armhf (2.1.12-stable-1) ...
Setting up liblapack3:armhf (3.10.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libxcb1:armhf (1.14-3) ...
Setting up gettext (0.21-4) ...
Setting up libfftw3-single3:armhf (3.3.8-2) ...
Setting up libxau-dev:armhf (1:1.0.9-1) ...
Setting up libtool (2.4.6-15) ...
Setting up libarchive13:armhf (3.4.3-2) ...
Setting up libfftw3-bin (3.3.8-2) ...
Setting up libgcc-10-dev:armhf (10.3.0-11+rpi1) ...
Setting up libedit2:armhf (3.1-20210910-1) ...
Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-1) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libnuma-dev:armhf (2.0.14-3) ...
Setting up libnl-route-3-200:armhf (3.4.0-1) ...
Setting up libxdmcp-dev:armhf (1:1.1.2-3) ...
Setting up libjs-jquery-ui (1.12.1+dfsg-8) ...
Setting up libevent-dev (2.1.12-stable-1) ...
Setting up liblapack-dev:armhf (3.10.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up gcc-10 (10.3.0-11+rpi1) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.0-2) ...
Setting up dwz (0.14-1) ...
Setting up libnl-3-dev:armhf (3.4.0-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up procps (2:3.3.17-5) ...
Setting up libcurl4:armhf (7.74.0-1.3) ...
Setting up libx11-6:armhf (2:1.7.2-2) ...
Setting up libgfortran-10-dev:armhf (10.3.0-11+rpi1) ...
Setting up libfftw3-dev:armhf (3.3.8-2) ...
Setting up python3.9 (3.9.7-4+rpi1) ...
Setting up automake (1:1.16.5-1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libibverbs1:armhf (36.0-1) ...
Setting up libstdc++-10-dev:armhf (10.3.0-11+rpi1) ...
Setting up libboost1.74-dev:armhf (1.74.0-9) ...
Setting up libxcb1-dev:armhf (1.14-3) ...
Setting up g++-10 (10.3.0-11+rpi1) ...
Setting up ibverbs-providers:armhf (36.0-1) ...
Setting up openssh-client (1:8.4p1-6) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libx11-dev:armhf (2:1.7.2-2) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up python3 (3.9.2-3) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxnvctrl0:armhf (470.57.02-2) ...
Setting up dh-autoreconf (20) ...
Setting up libnl-route-3-dev:armhf (3.4.0-1) ...
Setting up libltdl-dev:armhf (2.4.6-15) ...
Setting up gfortran-10 (10.3.0-11+rpi1) ...
Setting up cmake (3.21.3-5) ...
Setting up libhwloc-dev:armhf (2.5.0+dfsg-2) ...
Setting up libboost-dev:armhf (1.74.0.3+b1) ...
Setting up lsb-release (11.1.0+rpi1) ...
Setting up librdmacm1:armhf (36.0-1) ...
Setting up debhelper (13.5.2) ...
Setting up libibverbs-dev:armhf (36.0-1) ...
Setting up libhwloc-plugins:armhf (2.5.0+dfsg-2) ...
Setting up libfabric1 (1.11.0-2) ...
Setting up libpmix2:armhf (4.1.1~rc4-1) ...
Setting up libopenmpi3:armhf (4.1.2~rc1-4+rpi1) ...
Setting up libpmix-dev:armhf (4.1.1~rc4-1) ...
Setting up openmpi-bin (4.1.2~rc1-4+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up mpi-default-bin (1.14) ...
Setting up libopenmpi-dev:armhf (4.1.2~rc1-4+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up mpi-default-dev (1.14) ...
Setting up sbuild-build-depends-gromacs-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-11+rpi1 gcc-10_10.3.0-11+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++6_11.2.0-9+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.5-1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-1 build-essential_12.9 bzip2_1.0.8-4 chrpath_0.16-2 cmake_3.21.3-5 cmake-data_3.21.3-5 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-11+rpi1 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-elpa-helper_2.0.9 dh-strip-nondeterminism_1.12.0-2 diffutils_1:3.7-5 dirmngr_2.2.27-2 distro-info-data_0.52 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 emacsen-common_3.0.4 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-11+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-11+rpi1 gcc-10-base_10.3.0-11+rpi1 gcc-11-base_11.2.0-9+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gfortran-10_10.3.0-11+rpi1 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 ibverbs-providers_36.0-1 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libasan6_11.2.0-9+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-9+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbinutils_2.37-5+rpi1 libblas-dev_3.10.0-1 libblas3_3.10.0-1 libblkid1_2.37.2-1 libboost-dev_1.74.0.3+b1 libboost1.74-dev_1.74.0-9 libbrotli1_1.0.9-2+b1 libbsd0_0.11.3-1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcbor0_0.5.0+dfsg-2 libcc1-0_11.2.0-9+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libcurl4_7.74.0-1.3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9+rpi1 libedit2_3.1-20210910-1 libelf1_0.185-2 libevent-2.1-7_2.1.12-stable-1 libevent-core-2.1-7_2.1.12-stable-1 libevent-dev_2.1.12-stable-1 libevent-extra-2.1-7_2.1.12-stable-1 libevent-openssl-2.1-7_2.1.12-stable-1 libevent-pthreads-2.1-7_2.1.12-stable-1 libexpat1_2.4.1-2 libext2fs2_1.46.4-1 libfabric1_1.11.0-2 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libffi8_3.4.2-3 libfftw3-bin_3.3.8-2 libfftw3-dev_3.3.8-2 libfftw3-double3_3.3.8-2 libfftw3-single3_3.3.8-2 libfido2-1_1.8.0-1 libfile-stripnondeterminism-perl_1.12.0-2 libgcc-10-dev_10.3.0-11+rpi1 libgcc-s1_11.2.0-9+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgfortran-10-dev_10.3.0-11+rpi1 libgfortran5_11.2.0-9+rpi1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-9+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libhwloc-dev_2.5.0+dfsg-2 libhwloc-plugins_2.5.0+dfsg-2 libhwloc15_2.5.0+dfsg-2 libibverbs-dev_36.0-1 libibverbs1_36.0-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.23-1 libjs-jquery_3.5.1+dfsg+~3.5.5-7 libjs-jquery-ui_1.12.1+dfsg-8 libjsoncpp24_1.9.4-5 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 liblapack-dev_3.10.0-1 liblapack3_3.10.0-1 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 libltdl-dev_2.4.6-15 libltdl7_2.4.6-15 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmd0_1.0.4-1 libmount1_2.37.2-1 libmpc3_1.2.0-1 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-4 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnuma-dev_2.0.14-3 libnuma1_2.0.14-3 libopenmpi-dev_4.1.2~rc1-4+rpi1 libopenmpi3_4.1.2~rc1-4+rpi1 libp11-kit0_0.24.0-2 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpciaccess0_0.16-1 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-5 libpipeline1_1.5.3-1 libpmix-dev_4.1.1~rc4-1 libpmix2_4.1.1~rc4-1 libprocps8_2:3.3.17-5 libpsl5_0.21.0-1.2 libpthread-stubs0-dev_0.4-1 libpython3-stdlib_3.9.2-3 libpython3.9-minimal_3.9.7-4+rpi1 libpython3.9-stdlib_3.9.7-4+rpi1 librdmacm1_36.0-1 libreadline8_8.1-2 librhash0_1.4.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-1 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssh2-1_1.10.0-2 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++6_11.2.0-9+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.9-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-9+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-1 libuv1_1.42.0-1 libx11-6_2:1.7.2-2 libx11-data_2:1.7.2-2 libx11-dev_2:1.7.2-2 libxau-dev_1:1.0.9-1 libxau6_1:1.0.9-1 libxcb1_1.14-3 libxcb1-dev_1.14-3 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxml2_2.9.12+dfsg-5 libxnvctrl0_470.57.02-2 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 lsb-release_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.37.2-1 mpi-default-bin_1.14 mpi-default-dev_1.14 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 ocl-icd-libopencl1_2.2.14-3 openmpi-bin_4.1.2~rc1-4+rpi1 openmpi-common_4.1.2~rc1-4+rpi1 openssh-client_1:8.4p1-6 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 procps_2:3.3.17-5 python3_3.9.2-3 python3-minimal_3.9.2-3 python3.9_3.9.7-4+rpi1 python3.9-minimal_3.9.7-4+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gromacs-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.37.2-1 x11proto-dev_2021.5-1 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.foY7NTXm/trustedkeys.kbx': General error
gpgv: Signature made Sat Oct 23 18:30:34 2021 UTC
gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F
gpgv: issuer "nbreen@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./gromacs_2021.3-4.dsc
dpkg-source: info: extracting gromacs in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking gromacs_2021.3.orig.tar.gz
dpkg-source: info: unpacking gromacs_2021.3.orig-regressiontests.tar.gz
dpkg-source: info: unpacking gromacs_2021.3-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying readme.patch
dpkg-source: info: applying copyright-file.patch
dpkg-source: info: applying disable-cpuinfotest.patch
dpkg-source: info: applying mdrun-test-timeout.patch
dpkg-source: info: applying local-mathjax.patch
dpkg-source: info: applying mpi-tests-localhost.patch
dpkg-source: info: applying i386-disable-specific-tests.patch
dpkg-source: info: applying hppa-disable-ewaldunittest.patch
dpkg-source: info: applying manual-image-conversion.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-816283cf-9b1a-415c-bb32-0ec987687141
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package gromacs
dpkg-buildpackage: info: source version 2021.3-4
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh_testdir
dh_testroot
rm -rf build docs/doxygen/*.pyc
dh_clean build-basic build-mpi build-manual configure-stamp
debian/rules binary-arch
dh_testdir
(mkdir -p build/basic; cd build/basic; cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2021.3-4" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DGMX_INSTALL_LEGACY_API=ON )
-- The C compiler identification is GNU 10.3.0
-- The CXX compiler identification is GNU 10.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python3: /usr/bin/python3.9 (found suitable version "3.9.7", minimum required is "3.6") found components: Interpreter
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Using default binary suffix: ""
-- Using default library suffix: ""
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.5.0", minimum required is "1.5")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test TEST_ATOMICS
-- Performing Test TEST_ATOMICS - Success
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - not present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- Found LAPACK: /usr/lib/arm-linux-gnueabihf/liblapack.so;/usr/lib/arm-linux-gnueabihf/libblas.so
-- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1")
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic
(mkdir -p build/basic-dp; cd build/basic-dp; cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2021.3-4" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DGMX_DOUBLE=ON)
-- The C compiler identification is GNU 10.3.0
-- The CXX compiler identification is GNU 10.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python3: /usr/bin/python3.9 (found suitable version "3.9.7", minimum required is "3.6") found components: Interpreter
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Using default binary suffix: "_d"
-- Using default library suffix: "_d"
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.5.0", minimum required is "1.5")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test TEST_ATOMICS
-- Performing Test TEST_ATOMICS - Success
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - not present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- Found LAPACK: /usr/lib/arm-linux-gnueabihf/liblapack.so;/usr/lib/arm-linux-gnueabihf/libblas.so
-- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1")
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic-dp
(mkdir -p build/mpi; cd build/mpi; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2021.3-4" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi" -DGMX_LIBS_SUFFIX="_mpi")
-- The C compiler identification is GNU 10.3.0
-- The CXX compiler identification is GNU 10.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/mpicc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/mpicxx - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python3: /usr/bin/python3.9 (found suitable version "3.9.7", minimum required is "3.6") found components: Interpreter
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Using manually set binary suffix: "_mpi"
-- Using manually set library suffix: "_mpi"
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.5.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test TEST_ATOMICS
-- Performing Test TEST_ATOMICS - Success
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - not present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- Found LAPACK: /usr/lib/arm-linux-gnueabihf/liblapack.so;/usr/lib/arm-linux-gnueabihf/libblas.so
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- The mdrun-only build is deprecated
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpi
(mkdir -p build/mpi-dp; cd build/mpi-dp; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2021.3-4" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d" -DGMX_LIBS_SUFFIX="_mpi_d")
-- The C compiler identification is GNU 10.3.0
-- The CXX compiler identification is GNU 10.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/mpicc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/mpicxx - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python3: /usr/bin/python3.9 (found suitable version "3.9.7", minimum required is "3.6") found components: Interpreter
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Using manually set binary suffix: "_mpi_d"
-- Using manually set library suffix: "_mpi_d"
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.5.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test TEST_ATOMICS
-- Performing Test TEST_ATOMICS - Success
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - not present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- Found LAPACK: /usr/lib/arm-linux-gnueabihf/liblapack.so;/usr/lib/arm-linux-gnueabihf/libblas.so
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- The mdrun-only build is deprecated
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpi-dp
touch configure-stamp
dh_testdir
/usr/bin/make -j4 -C build/basic
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles /<<PKGBUILDDIR>>/build/basic//CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3.9 -D HAVE_FULL_FUNCTIONING_PYTHON=Python3_Interpreter_FOUND -D PROJECT_VERSION=2021.3-Raspbian-2021.3-4 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2021.3-4 -D SOURCE_IS_SOURCE_DISTRIBUTION=ON -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoWithoutGit.cmake
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++17 -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 0%] Built target release-version-info
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/alltoall.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_protocol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/barrier.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++17 -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_send_recv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/bcast.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_wait.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/collective.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/profile.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/comm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce.cpp
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++17 -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/event.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce_fast.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/gather.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scatter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/group.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_init.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/topology.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 0%] Built target lmfit_objlib
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/list.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/type.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 0%] Built target scanner
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scan.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 3%] Built target thread_mpi
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/nrjac.cpp.o -MF CMakeFiles/linearalgebra.dir/nrjac.cpp.o.d -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 3%] Built target linearalgebra
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /<<PKGBUILDDIR>>/src/programs/gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /<<PKGBUILDDIR>>/src/programs/legacymodules.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 3%] Built target gmx_objlib
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/3dview.cpp.o -MF CMakeFiles/view_objlib.dir/view/3dview.cpp.o.d -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/3dview.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/buttons.cpp.o -MF CMakeFiles/view_objlib.dir/view/buttons.cpp.o.d -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/buttons.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -MF CMakeFiles/view_objlib.dir/view/dialogs.cpp.o.d -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/dialogs.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 3%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -MF CMakeFiles/view_objlib.dir/view/fgrid.cpp.o.d -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/fgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/filter.cpp.o -MF CMakeFiles/view_objlib.dir/view/filter.cpp.o.d -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/filter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energydata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/logo.cpp.o -MF CMakeFiles/view_objlib.dir/view/logo.cpp.o.d -o CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/logo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o -MF CMakeFiles/modularsimulator.dir/forceelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/manager.cpp.o -MF CMakeFiles/view_objlib.dir/view/manager.cpp.o.d -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/molps.cpp.o -MF CMakeFiles/view_objlib.dir/view/molps.cpp.o.d -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/molps.cpp
[ 6%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -MF CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o.d -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/nleg.cpp.o -MF CMakeFiles/view_objlib.dir/view/nleg.cpp.o.d -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/nmol.cpp.o -MF CMakeFiles/view_objlib.dir/view/nmol.cpp.o.d -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -MF CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o.d -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/popup.cpp.o -MF CMakeFiles/view_objlib.dir/view/popup.cpp.o.d -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -MF CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -MF CMakeFiles/view_objlib.dir/view/pulldown.cpp.o.d -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/pulldown.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o -MF CMakeFiles/view_objlib.dir/view/view.cpp.o.d -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o -MF CMakeFiles/modularsimulator.dir/propagator.cpp.o.d -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o -MF CMakeFiles/modularsimulator.dir/signallers.cpp.o.d -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/x11.cpp.o -MF CMakeFiles/view_objlib.dir/view/x11.cpp.o.d -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -MF CMakeFiles/view_objlib.dir/view/xdlg.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/simulatoralgorithm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -MF CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -MF CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xmb.cpp.o -MF CMakeFiles/view_objlib.dir/view/xmb.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xutil.cpp.o -MF CMakeFiles/view_objlib.dir/view/xutil.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 7%] Built target view_objlib
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 9%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/filestream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/futil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/futil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/init.cpp.o -MF CMakeFiles/libgromacs.dir/utility/init.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -MF CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetree.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreemdpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/logger.cpp.o -MF CMakeFiles/libgromacs.dir/utility/logger.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/loggerbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/niceheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/path.cpp.o -MF CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -MF CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -MF CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -MF CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/smalloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strdb.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strdb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textreader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function '_ZN11PairlistSet18constructPairlistsERKN5Nbnxm7GridSetEN3gmx8ArrayRefI14PairsearchWorkEEP16nbnxn_atomdata_tRKNS4_11ListOfListsIiEEiP6t_nrnbP19SearchCycleCounting._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'void PairlistSet::constructPairlists(const Nbnxm::GridSet&, gmx::ArrayRef<PairsearchWork>, nbnxn_atomdata_t*, const gmx::ListOfLists<int>&, int, t_nrnb*, SearchCycleCounting*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/box.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/box.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/collect.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/partition.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/utility.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -MF CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o.d -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -MF CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o.d -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -MF CMakeFiles/libgromacs.dir/math/do_fit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -MF CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o.d -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/functions.cpp.o -MF CMakeFiles/libgromacs.dir/math/functions.cpp.o.d -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -MF CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o.d -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/matrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/matrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -MF CMakeFiles/libgromacs.dir/math/neldermead.cpp.o.d -o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/neldermead.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/optimization.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/units.cpp.o -MF CMakeFiles/libgromacs.dir/math/units.cpp.o.d -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/energyhistory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcebuffers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -Wno-class-memaccess -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/energyhistory.cpp:43:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h: In member function 'std::enable_if_t<gmx::IsSerializableType<T>::value, void> gmx::CheckpointData<gmx::CheckpointDataOperation::Read>::arrayRef(const string&, gmx::ArrayRef<T>) const [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h:442:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
442 | ReadCheckpointData::arrayRef(const std::string& key, ArrayRef<T> values) const
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/interaction_const.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/multipletimestepping.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:63:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h: In member function 'std::enable_if_t<gmx::IsSerializableType<T>::value, void> gmx::CheckpointData<gmx::CheckpointDataOperation::Read>::arrayRef(const string&, gmx::ArrayRef<T>) const [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h:442:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
442 | ReadCheckpointData::arrayRef(const std::string& key, ArrayRef<T> values) const
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:41:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:41:
/usr/include/c++/10/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -MF CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:368:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
368 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -MF CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -MF CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atoms.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -MF CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -MF CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -MF CMakeFiles/libgromacs.dir/topology/invblock.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -MF CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -MF CMakeFiles/libgromacs.dir/topology/symtab.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topology.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topology.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topsort.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -MF CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o.d -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/output.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/output.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pull.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
2297 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/simd/support.cpp.o -MF CMakeFiles/libgromacs.dir/simd/support.cpp.o.d -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/anadih.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/angle_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/binsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/cmat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dens_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dlist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/eigio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/fitahx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_anaeig.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_analyze.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bundle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_chi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_confrms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_covar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_current.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_density.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densmap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densorder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dielectric.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dipoles.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_disre.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_mapping&}; _Tp = t_mapping; _Alloc = std::allocator<t_mapping>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_mapping>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void prune_ss_legend(t_matrix*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dos.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dyecoupl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_enemat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_gyrate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_h2order.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hbond.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helixorient.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hydorder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_lie.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_make_edi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mdmat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmeig.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmens.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_order.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_polystat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_potential.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_principal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rama.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsdist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotacf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotmat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saltbr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sans.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saxs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sham.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sigeps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sorient.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spatial.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_tcaf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjorder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_vanhove.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_velacc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wham.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wheel.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/hxprops.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void rainbow_map(gmx_bool, gmx::ArrayRef<t_mapping>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1329:13: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1329 | static void rainbow_map(gmx_bool bBlue, gmx::ArrayRef<t_mapping> map)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void leg_continuous(t_psdata*, real, real, real, const string&, real, char*, gmx::ArrayRef<const t_mapping>, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:250:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
250 | static void leg_continuous(t_psdata* ps,
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nrama.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void ps_mat(const char*, gmx::ArrayRef<t_matrix>, gmx::ArrayRef<t_matrix>, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, int, real, real, real, const char*, const char*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1034:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
1034 | leg_continuous(&out, x0 + w / 2, w / 2, DDD, legend, psr->legfontsize, psr->legfont,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1035 | leg_map, mapoffset);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1034:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
317 | leg_continuous(ps, xx1, x1, y0, label1, fontsize, font, map1, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:318:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
318 | leg_continuous(ps, xx2, x2, y0, label2, fontsize, font, map2, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:318:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nsfactor.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'int gmx_xpm2ps(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1377:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1377 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1377:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1377 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/powerspect.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/pp2shift.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/princ.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/sfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/calch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/fflibutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genion.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genrestr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gmxcpp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hizzie.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pgutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function 'void process_pull_groups(gmx::ArrayRef<t_pull_group>, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, const t_blocka*, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:453:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'gmx::index' {aka 'int'} [-Wformat=]
453 | "Number of weights (%ld) for pull group %d '%s' does not match the number of "
| ~~^
| |
| long int
| %d
454 | "atoms (%ld)",
455 | gmx::ssize(pullGroup.weight), g, pullGroupNames[g].c_str(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| gmx::index {aka int}
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:454:33: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'gmx::index' {aka 'int'} [-Wformat=]
454 | "atoms (%ld)",
| ~~^
| |
| long int
| %d
455 | gmx::ssize(pullGroup.weight), g, pullGroupNames[g].c_str(),
456 | gmx::ssize(pullGroup.ind));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| gmx::index {aka int}
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readrot.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/xlate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/crosscorr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/gmx_lmcurve.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/integrate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/polynomials.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -MF CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o.d -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/statistics/statistics.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/abstractdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataproxy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/average.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/frameaverager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/histogram.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {float}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {float&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::AnalysisDataDisplacementModule::frameFinished(const gmx::AnalysisDataFrameHeader&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/plot.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::AnalysisDataValue&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::internal::AnalysisDataStorageFrameData::addPointSet(int, int, gmx::ArrayRef<const gmx::AnalysisDataValue>)':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:584:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
584 | void AnalysisDataStorageFrameData::addPointSet(int dataSetIndex,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::AnalysisDataStorageFrame::finishPointSet()':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:715:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
715 | data_->addPointSet(currentDataSet_, firstColumn,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
716 | makeConstArrayRef(values_).subArray(begin, end - begin));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:715:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/coordinatefile.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/outputselector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setforces.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setprecision.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setvelocities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/check.cpp.o -MF CMakeFiles/libgromacs.dir/tools/check.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/check.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -MF CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/convert_tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/dump.cpp.o -MF CMakeFiles/libgromacs.dir/tools/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/eneconv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/make_ndx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/mk_angndx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -MF CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/pme_error.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -MF CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjcat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -MF CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tune_pme.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energydrifttracker.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In member function 'void ForeignLambdaTerms::finalizePotentialContributions(gmx::ArrayRef<const double>, gmx::ArrayRef<const float>, const t_lambda&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:173:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
173 | void ForeignLambdaTerms::finalizePotentialContributions(gmx::ArrayRef<const double> dvdlLinear,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function 'void accumulatePotentialEnergies(gmx_enerdata_t*, gmx::ArrayRef<const float>, const t_lambda*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:235:65: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
235 | enerd->foreignLambdaTerms.finalizePotentialContributions(enerd->dvdl_lin, lambda, *fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/freeenergyparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gpuforcereduction_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, gmx::ImdSession*, pull_t*, int64_t, t_nrnb*, gmx_wallcycle_t, const gmx_localtop_t*, const real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<float> >, history_t*, gmx::ForceBuffersView*, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, gmx::ArrayRef<const float>, t_forcerec*, gmx::MdrunScheduleWorkload*, gmx::VirtualSitesHandler*, real*, double, gmx_edsam*, int, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:645:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
645 | enerd->foreignLambdaTerms.finalizePotentialContributions(enerd->dvdl_lin, lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
646 | *inputrec->fepvals);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:651:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
651 | enerd->term[F_COM_PULL] += awh->applyBiasForcesAndUpdateBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
652 | inputrec->pbcType, mdatoms->massT, foreignLambdaDeltaH, foreignLambdaDhDl, box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
653 | forceWithVirial, t, step, wcycle, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:651:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:651:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_gpu_impl.cpp: In member function 'void gmx::UpdateConstrainGpu::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_gpu_impl.cpp:73:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
73 | void UpdateConstrainGpu::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wholemoleculetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:396:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
396 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:396:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:418:45: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
418 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, neighborLambdaDhdl,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
419 | forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:418:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationgrid.h:105:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
105 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:105:29: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
105 | gmx::ArrayRef<const double> Bias::calcForceAndUpdateBias(const awh_dvec coordValue,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:105:29: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:105:29: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
146 | convolvedBias = state_.updateProbabilityWeightsAndConvolvedBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
147 | dimParams_, grid_, moveUmbrella ? neighborLambdaEnergies : ArrayRef<const double>{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | &probWeightNeighbor);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:152:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
152 | updateForceCorrelationGrid(probWeightNeighbor, neighborLambdaDhdl, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:152:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:152:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:154:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
154 | state_.sampleCoordAndPmf(dimParams_, grid_, probWeightNeighbor, convolvedBias);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:154:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
168 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
169 | moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
170 | tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
180 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
181 | dimParams_, grid_, coordState.umbrellaGridpoint(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
182 | moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{}, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
192 | state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, neighborLambdaDhdl,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
193 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
180 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
181 | dimParams_, grid_, coordState.umbrellaGridpoint(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
182 | moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{}, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
146 | convolvedBias = state_.updateProbabilityWeightsAndConvolvedBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
147 | dimParams_, grid_, moveUmbrella ? neighborLambdaEnergies : ArrayRef<const double>{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | &probWeightNeighbor);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp: In member function 'real gmx::Awh::applyBiasForcesAndUpdateBias(PbcType, const real*, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, const real (*)[3], gmx::ForceWithVirial*, double, int64_t, gmx_wallcycle*, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:294:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
294 | real Awh::applyBiasForcesAndUpdateBias(PbcType pbcType,
| ^~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:294:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:352:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
352 | &biasPotentialJump, commRecord_, multiSimRecord_, t, step, seed_, fplog);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:352:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:352:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.h:70,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:48:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasparams.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*, int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/memory:63,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.cpp:47:
/usr/include/c++/10/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >; _Predicate = __gnu_cxx::__ops::_Iter_pred<gmx::BiasGrid::hasLambdaAxis() const::<lambda(const auto:22&)> >]':
/usr/include/c++/10/bits/stl_algobase.h:1921:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
1921 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~
/usr/include/c++/10/bits/stl_algobase.h:1921:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algobase.h: In function 'bool gmx::pointsAlongLambdaAxis(const gmx::BiasGrid&, int, int)':
/usr/include/c++/10/bits/stl_algobase.h:1974:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
1974 | return __find_if(__first, __last, __pred,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
1975 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algobase.h: In function 'bool gmx::pointsHaveDifferentLambda(const gmx::BiasGrid&, int, int)':
/usr/include/c++/10/bits/stl_algobase.h:1974:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
1974 | return __find_if(__first, __last, __pred,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
1975 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biassharing.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/dimparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.h:61,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, int, const int&, bool}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::BiasGrid::BiasGrid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, int, int&, bool}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&, bool}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biaswriter.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::BiasGrid&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/coordstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:351:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
351 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, int, gmx::ArrayRef<const double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:475:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
475 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:475:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
508 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:529:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
529 | calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, neighborLambdaDhdl, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:529:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
539 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:549:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
549 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
550 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:549:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:553:69: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
553 | double newPotential = calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
554 | dimParams, grid, coordState_.umbrellaGridpoint(), neighborLambdaDhdl, newForce);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:553:69: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::BiasGrid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const BiasGrid& grid,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::BiasGrid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1350:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1350 | void BiasState::sampleProbabilityWeights(const BiasGrid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1404:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1404 | void BiasState::sampleCoordAndPmf(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationhistory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'double gmx::BiasState::updateProbabilityWeightsAndConvolvedBias(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >*) const':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1242:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1242 | double BiasState::updateProbabilityWeightsAndConvolvedBias(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/pointstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/read_params.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
78 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
210 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:243:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
243 | newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:243:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1159 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1160 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<float> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -MF CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/device_stream_manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/device_context.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/device_stream.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/device_management_common.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/prepare_detection.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/prepare_detection.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/prepare_detection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/prepare_detection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/device_management.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/md.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/membedholder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1289:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1289 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1290 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1291 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1292 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationinput.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationinputhandle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulatorbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -MF CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o.d -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -MF CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o.d -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -MF CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -MF CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o.d -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -MF CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o.d -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -MF CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/options.cpp.o -MF CMakeFiles/libgromacs.dir/options/options.cpp.o.d -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -MF CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o.d -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -MF CMakeFiles/libgromacs.dir/options/optionsection.cpp.o.d -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -MF CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o.d -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -MF CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -MF CMakeFiles/libgromacs.dir/options/treesupport.cpp.o.d -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/manager.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/confio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<float> >, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/espio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/groio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/matio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/md5.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:116:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
116 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -MF CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -MF CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionbehavior.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selelem.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selelem.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selhelp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selmethod.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selvalue.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_compare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_insolidangle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_keywords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_merge.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_permute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_position.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_same.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_simple.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/symrec.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs.so.6 -o ../../lib/libgromacs.so.6.0.0 CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o CMakeFiles/libgromacs.dir/utility/any.cpp.o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o CMakeFiles/libgromacs.dir/utility/compare.cpp.o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o CMakeFiles/libgromacs.dir/utility/futil.cpp.o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o CMakeFiles/libgromacs.dir/utility/init.cpp.o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o CMakeFiles/libgromacs.dir/utility/logger.cpp.o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o CMakeFiles/libgromacs.dir/utility/path.cpp.o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o CMakeFiles/libgromacs.dir/domdec/box.cpp.o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o CMakeFiles/libgromacs.dir/math/functions.cpp.o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o CMakeFiles/libgromacs.dir/math/matrix.cpp.o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o CMakeFiles/libgromacs.dir/math/optimization.cpp.o CMakeFiles/libgromacs.dir/math/units.cpp.o CMakeFiles/libgromacs.dir/math/utilities.cpp.o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o CMakeFiles/libgromacs.dir/random/seed.cpp.o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o CMakeFiles/libgromacs.dir/topology/block.cpp.o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o CMakeFiles/libgromacs.dir/topology/idef.cpp.o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o CMakeFiles/libgromacs.dir/topology/index.cpp.o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o CMakeFiles/libgromacs.dir/topology/topology.cpp.o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o CMakeFiles/libgromacs.dir/pulling/output.cpp.o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o CMakeFiles/libgromacs.dir/simd/support.cpp.o CMakeFiles/libgromacs.dir/imd/imd.cpp.o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o CMakeFiles/libgromacs.dir/tools/check.cpp.o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o CMakeFiles/libgromacs.dir/tools/dump.cpp.o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl.cpp.o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o CMakeFiles/libgromacs.dir/fft/fft.cpp.o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o CMakeFiles/libgromacs.dir/hardware/prepare_detection.cpp.o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o CMakeFiles/libgromacs.dir/options/options.cpp.o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o CMakeFiles/libgromacs.dir/selection/params.cpp.o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o CMakeFiles/libgromacs.dir/selection/position.cpp.o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o CMakeFiles/libgromacs.dir/selection/selection.cpp.o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/nrjac.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o selection/CMakeFiles/scanner.dir/parser.cpp.o selection/CMakeFiles/scanner.dir/scanner.cpp.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so -lpthread -lm /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.6.0.0 ../../lib/libgromacs.so.6 ../../lib/libgromacs.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target libgromacs
/usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend
/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend
/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/share/template /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/share/template /<<PKGBUILDDIR>>/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib /<<PKGBUILDDIR>>/build/basic/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/share/template && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -std=c++17 -MD -MT share/template/CMakeFiles/template.dir/template.cpp.o -MF CMakeFiles/template.dir/template.cpp.o.d -o CMakeFiles/template.dir/template.cpp.o -c /<<PKGBUILDDIR>>/share/template/template.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/box.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/forcecalculator.cpp.o -MF CMakeFiles/nblib.dir/forcecalculator.cpp.o.d -o CMakeFiles/nblib.dir/forcecalculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx ../../lib/libgromacs.so.6.0.0 /usr/lib/arm-linux-gnueabihf/libX11.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target gmx
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxsetup.cpp.o -MF CMakeFiles/nblib.dir/gmxsetup.cpp.o.d -o CMakeFiles/nblib.dir/gmxsetup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/integrator.cpp
cd /<<PKGBUILDDIR>>/build/basic/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/template.dir/template.cpp.o -o ../../bin/template ../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target template
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/particlesequencer.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/particletype.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/simulationstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/topologyhelpers.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/transformations.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/util/setup.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib.so.0 -o ../../lib/libnblib.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/forcecalculator.cpp.o CMakeFiles/nblib.dir/gmxcalculator.cpp.o CMakeFiles/nblib.dir/gmxsetup.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o ../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib.so.0.1.0 ../../lib/libnblib.so.0 ../../lib/libnblib.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target nblib
/usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend
/usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/samples /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib/samples /<<PKGBUILDDIR>>/build/basic/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/samples /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib/samples /<<PKGBUILDDIR>>/build/basic/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build
/usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -o ../../../bin/argon-forces-integration ../../../lib/libnblib.so.0.1.0 -Wl,-rpath-link,/<<PKGBUILDDIR>>/build/basic/lib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target argon-forces-integration
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -o ../../../bin/methane-water-integration ../../../lib/libnblib.so.0.1.0 -Wl,-rpath-link,/<<PKGBUILDDIR>>/build/basic/lib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target methane-water-integration
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -j4 -C build/basic-dp
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles /<<PKGBUILDDIR>>/build/basic-dp//CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3.9 -D HAVE_FULL_FUNCTIONING_PYTHON=Python3_Interpreter_FOUND -D PROJECT_VERSION=2021.3-Raspbian-2021.3-4 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2021.3-4 -D SOURCE_IS_SOURCE_DISTRIBUTION=ON -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoWithoutGit.cmake
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++17 -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 0%] Built target release-version-info
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++17 -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/alltoall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_protocol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/barrier.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_send_recv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/bcast.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_wait.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/collective.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++17 -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/profile.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/comm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/event.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce_fast.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/gather.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scatter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/group.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 0%] Built target lmfit_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_init.cpp
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/list.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/type.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 0%] Built target scanner
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scan.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 3%] Built target thread_mpi
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/nrjac.cpp.o -MF CMakeFiles/linearalgebra.dir/nrjac.cpp.o.d -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 3%] Built target linearalgebra
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp: In member function 'void gmx::ConstraintsElement<variable>::apply(gmx::Step, bool, bool, bool) [with gmx::ConstraintVariable variable = gmx::ConstraintVariable::Positions]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp:158:19: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
158 | constr_->apply(writeLog, writeEnergy, step, 1, 1.0, x, xprime, min_proj, statePropagatorData_->box(),
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
159 | lambdaBonded, &dvdlambda, v, calculateVirial, vir_con, variable);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp: In member function 'void gmx::ComputeGlobalsElement<algorithm>::compute(gmx::Step, unsigned int, gmx::SimulationSignaller*, bool, bool) [with gmx::ComputeGlobalsAlgorithm algorithm = gmx::ComputeGlobalsAlgorithm::LeapFrog]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:284:20: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
284 | compute_globals(
| ~~~~~~~~~~~~~~~^
285 | gstat_, cr_, inputrec_, fr_, energyData_->ekindata(), x, v, box, mdAtoms_->mdatoms(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
286 | nrnb_, &vcm_, step != -1 ? wcycle_ : nullptr, energyData_->enerdata(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
287 | energyData_->forceVirial(step), energyData_->constraintVirial(step),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
288 | energyData_->totalVirial(step), energyData_->pressure(step), constr_, signaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
289 | lastbox, &totalNumberOfBondedInteractions_, energyData_->needToSumEkinhOld(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
290 | flags | (shouldCheckNumberOfBondedInteractions_ ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:284:20: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:291:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
291 | checkNumberOfBondedInteractions(mdlog_, cr_, totalNumberOfBondedInteractions_, top_global_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
292 | localTopology_, x, box, &shouldCheckNumberOfBondedInteractions_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:295:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
295 | process_and_stopcm_grp(fplog_, &vcm_, *mdAtoms_->mdatoms(), x, v);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:295:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:295:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp: In member function 'void gmx::ComputeGlobalsElement<algorithm>::elementSetup() [with gmx::ComputeGlobalsAlgorithm algorithm = gmx::ComputeGlobalsAlgorithm::LeapFrog]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:140:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
140 | process_and_stopcm_grp(fplog_, &vcm_, *mdAtoms_->mdatoms(), x.unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
141 | v.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:140:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:140:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp: In member function 'void gmx::ConstraintsElement<variable>::apply(gmx::Step, bool, bool, bool) [with gmx::ConstraintVariable variable = gmx::ConstraintVariable::Velocities]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp:158:19: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
158 | constr_->apply(writeLog, writeEnergy, step, 1, 1.0, x, xprime, min_proj, statePropagatorData_->box(),
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
159 | lambdaBonded, &dvdlambda, v, calculateVirial, vir_con, variable);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp: In member function 'void gmx::ComputeGlobalsElement<algorithm>::compute(gmx::Step, unsigned int, gmx::SimulationSignaller*, bool, bool) [with gmx::ComputeGlobalsAlgorithm algorithm = gmx::ComputeGlobalsAlgorithm::VelocityVerlet]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:284:20: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
284 | compute_globals(
| ~~~~~~~~~~~~~~~^
285 | gstat_, cr_, inputrec_, fr_, energyData_->ekindata(), x, v, box, mdAtoms_->mdatoms(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
286 | nrnb_, &vcm_, step != -1 ? wcycle_ : nullptr, energyData_->enerdata(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
287 | energyData_->forceVirial(step), energyData_->constraintVirial(step),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
288 | energyData_->totalVirial(step), energyData_->pressure(step), constr_, signaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
289 | lastbox, &totalNumberOfBondedInteractions_, energyData_->needToSumEkinhOld(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
290 | flags | (shouldCheckNumberOfBondedInteractions_ ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:284:20: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:291:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
291 | checkNumberOfBondedInteractions(mdlog_, cr_, totalNumberOfBondedInteractions_, top_global_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
292 | localTopology_, x, box, &shouldCheckNumberOfBondedInteractions_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:295:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
295 | process_and_stopcm_grp(fplog_, &vcm_, *mdAtoms_->mdatoms(), x, v);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:295:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:295:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp: In member function 'void gmx::ComputeGlobalsElement<algorithm>::elementSetup() [with gmx::ComputeGlobalsAlgorithm algorithm = gmx::ComputeGlobalsAlgorithm::VelocityVerlet]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:140:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
140 | process_and_stopcm_grp(fplog_, &vcm_, *mdAtoms_->mdatoms(), x.unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
141 | v.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:140:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:140:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /<<PKGBUILDDIR>>/src/programs/gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /<<PKGBUILDDIR>>/src/programs/legacymodules.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 3%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energydata.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 3%] Built target gmx_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o -MF CMakeFiles/modularsimulator.dir/forceelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/3dview.cpp.o -MF CMakeFiles/view_objlib.dir/view/3dview.cpp.o.d -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/3dview.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/buttons.cpp.o -MF CMakeFiles/view_objlib.dir/view/buttons.cpp.o.d -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/buttons.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -MF CMakeFiles/view_objlib.dir/view/dialogs.cpp.o.d -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/dialogs.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energydata.cpp: In member function 'void gmx::EnergyData::doStep(gmx::Time, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energydata.cpp:241:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
241 | accumulateKineticLambdaComponents(enerd_, freeEnergyPerturbationData_->constLambdaView(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
242 | *inputrec_->fepvals);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp: In member function 'void gmx::ForceElement::run(gmx::Step, gmx::Time, unsigned int) [with bool doShellFC = true]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp:197:28: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
197 | relax_shell_flexcon(
| ~~~~~~~~~~~~~~~~~~~^
198 | fplog_, cr_, ms, isVerbose_, enforcedRotation_, step, inputrec_, imdSession_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
199 | pull_work_, step == nextNSStep_, static_cast<int>(flags), localTopology_, constr_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | energyData_->enerdata(), statePropagatorData_->localNumAtoms(), x, v, box, lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | hist, &forces, force_vir, mdAtoms_->mdatoms(), nrnb_, wcycle_, shellfc_, fr_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
202 | runScheduleWork_, time, energyData_->muTot(), vsite_, ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp: In member function 'void gmx::ForceElement::run(gmx::Step, gmx::Time, unsigned int) [with bool doShellFC = false]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp:211:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | do_force(fplog_, cr_, ms, inputrec_, awh, enforcedRotation_, imdSession_, pull_work_, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
212 | nrnb_, wcycle_, localTopology_, box, x, hist, &forces, force_vir,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
213 | mdAtoms_->mdatoms(), energyData_->enerdata(), lambda, fr_, runScheduleWork_, vsite_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
214 | energyData_->muTot(), time, ed, static_cast<int>(flags), ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -MF CMakeFiles/view_objlib.dir/view/fgrid.cpp.o.d -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/fgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/filter.cpp.o -MF CMakeFiles/view_objlib.dir/view/filter.cpp.o.d -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/logo.cpp.o -MF CMakeFiles/view_objlib.dir/view/logo.cpp.o.d -o CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/logo.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 6%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -MF CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o.d -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/manager.cpp.o -MF CMakeFiles/view_objlib.dir/view/manager.cpp.o.d -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/molps.cpp.o -MF CMakeFiles/view_objlib.dir/view/molps.cpp.o.d -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/molps.cpp
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp: In function 'bool ManCallBack(t_x11*, XEvent*, Window, void*)':
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:367:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
367 | put_atoms_in_compact_unitcell(man->molw->pbcType, ecenterDEF, man->box, atomsArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:367:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/nleg.cpp.o -MF CMakeFiles/view_objlib.dir/view/nleg.cpp.o.d -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp: In constructor 'gmx::FreeEnergyPerturbationData::FreeEnergyPerturbationData(FILE*, const t_inputrec*, gmx::MDAtoms*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp:75:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
75 | initialize_lambdas(fplog_, *inputrec_, true, ¤tFEPState_, lambda_);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/nmol.cpp.o -MF CMakeFiles/view_objlib.dir/view/nmol.cpp.o.d -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -MF CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o.d -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -MF CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/popup.cpp.o -MF CMakeFiles/view_objlib.dir/view/popup.cpp.o.d -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -MF CMakeFiles/view_objlib.dir/view/pulldown.cpp.o.d -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/pulldown.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp: In member function 'void gmx::PmeLoadBalanceHelper::run(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp:108:19: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
108 | pme_loadbal_do(pme_loadbal_, cr_, (isVerbose_ && MASTER(cr_)) ? stderr : nullptr, fplog_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
109 | mdlog_, *inputrec_, fr_, statePropagatorData_->constBox(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
110 | statePropagatorData_->constPositionsView().paddedArrayRef(), wcycle_, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
111 | step - inputrec_->init_step, &bPMETunePrinting_, false);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o -MF CMakeFiles/modularsimulator.dir/propagator.cpp.o.d -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o -MF CMakeFiles/view_objlib.dir/view/view.cpp.o.d -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o -MF CMakeFiles/modularsimulator.dir/signallers.cpp.o.d -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/x11.cpp.o -MF CMakeFiles/view_objlib.dir/view/x11.cpp.o.d -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -MF CMakeFiles/view_objlib.dir/view/xdlg.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/simulatoralgorithm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -MF CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -MF CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xmb.cpp.o -MF CMakeFiles/view_objlib.dir/view/xmb.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::Element::_ZN3gmx19StatePropagatorData7Element24trajectoryWriterTeardownEP10gmx_mdoutf.part.0(gmx_mdoutf*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:605:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
605 | dd_collect_vec(cr_->dd, localStateBackup_->ddp_count, localStateBackup_->ddp_count_cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
606 | localStateBackup_->cg_gl, localStateBackup_->x, globalXRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:605:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:609:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
609 | dd_collect_vec(cr_->dd, localStateBackup_->ddp_count, localStateBackup_->ddp_count_cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
610 | localStateBackup_->cg_gl, localStateBackup_->v, globalVRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:609:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/xutil.cpp.o -MF CMakeFiles/view_objlib.dir/view/xutil.cpp.o.d -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::Element::write(gmx_mdoutf_t, gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:440:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
440 | mdoutf_write_to_trajectory_files(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
441 | fplog_, cr_, outf, static_cast<int>(mdof_flags), statePropagatorData_->totalNumAtoms_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
442 | currentStep, currentTime, localStateBackup_.get(), statePropagatorData_->globalState_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
443 | observablesHistory, statePropagatorData_->f_.view().force(), &dummyCheckpointDataHolder_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 7%] Built target view_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h: In member function 'void gmx::CheckpointData<gmx::CheckpointDataOperation::Read>::arrayRef(const string&, gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h:469:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
469 | inline void ReadCheckpointData::arrayRef(const std::string& key, ArrayRef<RVec> values) const
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h: In member function 'void gmx::CheckpointData<gmx::CheckpointDataOperation::Write>::arrayRef(const string&, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h:485:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
485 | inline void WriteCheckpointData::arrayRef(const std::string& key, ArrayRef<const RVec> values)
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::PaddedVector<T, Allocator>::resizeWithPadding(gmx::PaddedVector<T, Allocator>::size_type) [with T = gmx::BasicVector<double>; Allocator = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'virtual void gmx::StatePropagatorData::Element::saveCheckpointState(std::optional<gmx::CheckpointData<gmx::CheckpointDataOperation::Write> >, const t_commrec*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:510:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
510 | dd_collect_vec(cr->dd, statePropagatorData_->ddpCount_, statePropagatorData_->ddpCountCgGl_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
511 | statePropagatorData_->cgGl_, statePropagatorData_->x_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | statePropagatorData_->xGlobal_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:510:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:513:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
513 | dd_collect_vec(cr->dd, statePropagatorData_->ddpCount_, statePropagatorData_->ddpCountCgGl_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | statePropagatorData_->cgGl_, statePropagatorData_->v_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | statePropagatorData_->vGlobal_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:513:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::StatePropagatorData::setLocalState(std::unique_ptr<t_state>)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::StatePropagatorData::doCheckpointData(gmx::CheckpointData<operation>*) [with gmx::CheckpointDataOperation operation = gmx::CheckpointDataOperation::Read]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::StatePropagatorData::Element::restoreCheckpointState(std::optional<gmx::CheckpointData<gmx::CheckpointDataOperation::Read> >, const t_commrec*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::StatePropagatorData::StatePropagatorData(int, FILE*, const t_commrec*, t_state*, bool, bool, bool, const string&, const t_inputrec*, const t_mdatoms*, const gmx_mtop_t*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 9%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/filestream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/futil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/futil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/init.cpp.o -MF CMakeFiles/libgromacs.dir/utility/init.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -MF CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetree.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreemdpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/logger.cpp.o -MF CMakeFiles/libgromacs.dir/utility/logger.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/loggerbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/niceheader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/path.cpp.o -MF CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -MF CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -MF CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -MF CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/smalloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strdb.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strdb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textreader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function 'void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:1471:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1471 | void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t& nbat, gmx::ArrayRef<gmx::RVec> fshift)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp: In function 'void Nbnxm::setupAndRunInstance(const gmx::BenchmarkSystem&, const Nbnxm::KernelBenchOptions&, bool)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:208:24: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
208 | nbnxn_atomdata_init(gmx::MDLogger(), nbv->nbat.get(), kernelSetup.kernelType, combinationRule,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
209 | system.numAtomTypes, system.nonbondedParameters, 1, numThreads);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:229:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
229 | nbnxn_put_on_grid(nbv.get(), system.box, 0, lowerCorner, upperCorner, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
230 | { 0, int(system.coordinates.size()) }, atomDensity, atomInfo,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
231 | system.coordinates, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:235:27: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
235 | nbv->setAtomProperties(system.atomTypes, system.charges, atomInfo);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:235:27: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::fillCell(Nbnxm::GridSetData*, nbnxn_atomdata_t*, int, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, Nbnxm::BoundingBox*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:860:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
860 | void Grid::fillCell(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsCpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:988:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
988 | void Grid::sortColumnsCpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1028:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1028 | fillCell(gridSetData, nbat, atomOffsetCell, atomOffsetCell + numAtomsCell, atinfo, x, nullptr);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsGpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1051:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1051 | void Grid::sortColumnsGpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1152:29: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1152 | fillCell(gridSetData, nbat, atomOffsetX, atomOffsetX + numAtomsX, atinfo, x,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1153 | bb_work_aligned);
| ~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:51:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Nbnxm::KernelBenchOptions&}; _Tp = Nbnxm::KernelBenchOptions; _Alloc = std::allocator<Nbnxm::KernelBenchOptions>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Nbnxm::KernelBenchOptions>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function 'void nbnxn_atomdata_init(const gmx::MDLogger&, nbnxn_atomdata_t*, Nbnxm::KernelType, int, int, gmx::ArrayRef<const double>, int, int)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:623:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
623 | void nbnxn_atomdata_init(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:51:
/usr/include/c++/10/bits/stl_vector.h: In function 'void Nbnxm::bench(int, const Nbnxm::KernelBenchOptions&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In function '_ZN5Nbnxm4Grid14setCellIndicesEiiPNS_11GridSetDataEN3gmx8ArrayRefINS_8GridWorkEEENS3_5RangeIiEEPKiNS4_IKNS3_11BasicVectorIdEEEEiP16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1410:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1410 | sortColumnsGpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1411 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1405:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1405 | sortColumnsCpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1406 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In static member function 'static void Nbnxm::Grid::calcColumnIndices(const Nbnxm::Grid::Dimensions&, const gmx::UpdateGroupsCog*, gmx::Range<int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, int, int, gmx::ArrayRef<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1173:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1173 | void Grid::calcColumnIndices(const Grid::Dimensions& gridDims,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function 'void nbnxn_atomdata_set(nbnxn_atomdata_t*, const Nbnxm::GridSet&, gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, gmx::ArrayRef<const int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:955:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
955 | void nbnxn_atomdata_set(nbnxn_atomdata_t* nbat,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::setCellIndices(int, int, Nbnxm::GridSetData*, gmx::ArrayRef<Nbnxm::GridWork>, gmx::Range<int>, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1287 | void Grid::setCellIndices(int ddZone,
| ^~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In function '_ZN5Nbnxm7GridSet9putOnGridEPA3_KdiPS1_S4_PKN3gmx15UpdateGroupsCogENS5_5RangeIiEEdNS5_8ArrayRefIKiEENSB_IKNS5_11BasicVectorIdEEEEiPSC_P16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:215:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
215 | Grid::calcColumnIndices(grid.dimensions(), updateGroupsCog, atomRange, x, ddZone, move, thread,
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
216 | nthread, gridSetData_.cells, gridWork_[thread].numAtomsPerColumn);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In member function 'void Nbnxm::GridSet::putOnGrid(const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:135:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
135 | void GridSet::putOnGrid(const matrix box,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:222:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
222 | grid.setCellIndices(ddZone, cellOffset, &gridSetData_, gridWork_, atomRange, atomInfo.data(), x,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
223 | numAtomsMoved, nbat);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp: In member function 'void nonbonded_verlet_t::dispatchNonbondedKernel(gmx::InteractionLocality, const interaction_const_t&, const gmx::StepWorkload&, int, const t_forcerec&, gmx_enerdata_t*, t_nrnb*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp:446:33: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
446 | nbnxn_kernel_gpu_ref(
| ~~~~~~~~~~~~~~~~~~~~^
447 | pairlistSet.gpuList(), nbat.get(), &ic, fr.shift_vec, stepWork, clearF,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
448 | nbat->out[0].f, nbat->out[0].fshift.data(), enerd->grpp.ener[egCOULSR].data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
449 | fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp: In member function 'void nonbonded_verlet_t::dispatchFreeEnergyKernel(gmx::InteractionLocality, const t_forcerec*, real (*)[3], gmx::ForceWithShiftForces*, const t_mdatoms&, t_lambda*, gmx::ArrayRef<const double>, gmx_enerdata_t*, const gmx::StepWorkload&, t_nrnb*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp:458:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
458 | void nonbonded_verlet_t::dispatchFreeEnergyKernel(gmx::InteractionLocality iLocality,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp: In function 'void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu*, const nbnxn_atomdata_t*, const interaction_const_t*, real (*)[3], const gmx::StepWorkload&, int, gmx::ArrayRef<double>, real*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:58:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
58 | void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu* nbl,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid(nonbonded_verlet_t*, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:58:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
58 | void nbnxn_put_on_grid(nonbonded_verlet_t* nb_verlet,
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:54:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.h:197:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
197 | gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
198 | atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*, const gmx_domdec_zones_t*, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:77:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
77 | void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t* nbv,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:91:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
91 | nbnxn_put_on_grid(nbv, nullptr, zone, c0, c1, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
92 | { zones->cg_range[zone], zones->cg_range[zone + 1] }, -1, atomInfo, x, 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
93 | nullptr);
| ~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::setAtomProperties(gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, gmx::ArrayRef<const int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:122:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
122 | void nonbonded_verlet_t::setAtomProperties(gmx::ArrayRef<const int> atomTypes,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:122:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:23: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
126 | nbnxn_atomdata_set(nbat.get(), pairSearch_->gridSet(), atomTypes, atomCharges, atomInfo);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::convertCoordinates(gmx::AtomLocality, bool, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
129 | void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(gmx::AtomLocality, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:162:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
162 | void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp: In function 'std::unique_ptr<nonbonded_verlet_t> Nbnxm::init_nb_verlet(const gmx::MDLogger&, const t_inputrec*, const t_forcerec*, const t_commrec*, const gmx_hw_info_t&, bool, const gmx::DeviceStreamManager*, const gmx_mtop_t*, real (*)[3], gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp:431:24: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
431 | nbnxn_atomdata_init(mdlog, nbat.get(), kernelSetup.kernelType, enbnxninitcombrule, fr->ntype,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
432 | fr->nbfp, mimimumNumEnergyGroupNonbonded,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
433 | (useGpuForNonbonded || emulateGpu) ? 1 : gmx_omp_nthreads_get(emntNonbonded));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function '_ZN11PairlistSet18constructPairlistsERKN5Nbnxm7GridSetEN3gmx8ArrayRefI14PairsearchWorkEEP16nbnxn_atomdata_tRKNS4_11ListOfListsIiEEiP6t_nrnbP19SearchCycleCounting._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'void PairlistSet::constructPairlists(const Nbnxm::GridSet&, gmx::ArrayRef<PairsearchWork>, nbnxn_atomdata_t*, const gmx::ListOfLists<int>&, int, t_nrnb*, SearchCycleCounting*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::PinningPolicy}; _Tp = NbnxnPairlistGpu; _Alloc = std::allocator<NbnxnPairlistGpu>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<NbnxnPairlistGpu>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
/usr/include/c++/10/bits/vector.tcc: In constructor 'PairlistSet::PairlistSet(gmx::InteractionLocality, const PairlistParams&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/box.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/box.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, tmpi_comm_* const*, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:233:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
233 | static void low_set_ddbox(int numPbcDimensions,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:279:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
279 | void set_ddbox(const gmx_domdec_t& dd,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:292:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
292 | low_set_ddbox(dd.unitCellInfo.npbcdim, dd.unitCellInfo.numBoundedDimensions, &dd.numCells,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | box, calculateUnboundedSize, xRef,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
294 | needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr, ddbox);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:292:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(DDRole, MPI_Comm, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:303:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
303 | void set_ddbox_cr(DDRole ddRole,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:313:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
313 | low_set_ddbox(numPbcDimensions(ir.pbcType), inputrec2nboundeddim(&ir), dd_nc, box, true, x,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
314 | nullptr, ddbox);
| ~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/collect.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, int, int, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:231:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
231 | void dd_collect_vec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:231:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:296:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
296 | dd_collect_vec(dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
297 | state_local->x, globalXRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:296:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:302:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
302 | dd_collect_vec(dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
303 | state_local->v, globalVRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:302:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:308:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
308 | dd_collect_vec(dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
309 | state_local->cg_p, globalCgpRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:308:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp: In function 'void distributeVec(gmx_domdec_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:143:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
143 | static void distributeVec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:143:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp: In function 'void distributeState(const gmx::MDLogger&, gmx_domdec_t*, const gmx_mtop_t&, t_state*, const gmx_ddbox_t&, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:256:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
256 | distributeVec(dd, DDMASTER(dd) ? state->x : gmx::ArrayRef<const gmx::RVec>(), state_local->x);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:256:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:256:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:260:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
260 | distributeVec(dd, DDMASTER(dd) ? state->v : gmx::ArrayRef<const gmx::RVec>(), state_local->v);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:260:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:260:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:264:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
264 | distributeVec(dd, DDMASTER(dd) ? state->cg_p : gmx::ArrayRef<const gmx::RVec>(), state_local->cg_p);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:264:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:264:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp: In function 'void dd_move_x_constraints(gmx_domdec_t*, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp:106:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
106 | void dd_move_x_constraints(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp:106:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(const t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3074:17: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3074 | static gmx_bool test_dd_cutoff(const t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3083:14: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3083 | set_ddbox(*dd, false, box, true, x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool change_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3140:10: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3140 | gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void putUpdateGroupAtomsInSamePeriodicImage(const gmx_domdec_t&, const gmx_mtop_t&, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3225:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
3225 | void putUpdateGroupAtomsInSamePeriodicImage(const gmx_domdec_t& dd,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
118 | void ddSendrecv(const gmx_domdec_t* dd,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::Impl::Impl(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2967:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2967 | DomainDecompositionBuilder::Impl::Impl(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2167:38: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2167 | dd_bonded_cg_distance(mdlog, &mtop, &ir, xGlobal, box,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2168 | options.checkBondedInteractions, &r_2b, &r_mb);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2167:38: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3008:98: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3008 | systemInfo_, gridSetupCellsizeLimit, mtop_, ir_, box, xGlobal, &ddbox_);
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::DomainDecompositionBuilder(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3053:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3053 | DomainDecompositionBuilder::DomainDecompositionBuilder(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3061:76: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3061 | impl_(new Impl(mdlog, cr, options, mdrunOptions, mtop, ir, box, xGlobal))
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp: In function 'DDGridSetup getDDGridSetup(const gmx::MDLogger&, DDRole, MPI_Comm, int, const gmx::DomdecOptions&, const DDSettings&, const DDSystemInfo&, real, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:891:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
891 | DDGridSetup getDDGridSetup(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:912:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
912 | set_ddbox_cr(ddRole, communicator, &numDomainsLegacyIvec, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:916:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
916 | set_ddbox_cr(ddRole, communicator, nullptr, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:519:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
519 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:519:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:519:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:583:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
583 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:583:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:583:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:260:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
260 | void dd_move_x(gmx_domdec_t* dd, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_wallcycle* wcycle)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:337:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
337 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:337:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:337:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ForceWithShiftForces*, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:412:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
412 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:412:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:412:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp: In function 'void dd_move_f_vsites(const gmx_domdec_t&, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp:69:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
69 | void dd_move_f_vsites(const gmx_domdec_t& dd, gmx::ArrayRef<gmx::RVec> f, gmx::ArrayRef<gmx::RVec> fshift)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp:69:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp: In function 'void dd_clear_f_vsites(const gmx_domdec_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp:77:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
77 | void dd_clear_f_vsites(const gmx_domdec_t& dd, gmx::ArrayRef<gmx::RVec> f)
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp: In function 'void dd_print_missing_interactions(const gmx::MDLogger&, t_commrec*, int, const gmx_mtop_t*, const gmx_localtop_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:364:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
364 | void dd_print_missing_interactions(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp: In function 'void dd_bonded_cg_distance(const gmx::MDLogger&, const gmx_mtop_t*, const t_inputrec*, gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3], gmx_bool, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:1991:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1991 | void dd_bonded_cg_distance(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:53:
/usr/include/c++/10/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const t_iparams*, std::vector<t_iparams> >; <template-parameter-2-2> = void; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/stl_vector.h:1379:2: note: parameter passing for argument of type 'std::vector<t_iparams>::const_iterator' changed in GCC 7.1
1379 | insert(const_iterator __position, _InputIterator __first,
| ^~~~~~
/usr/include/c++/10/bits/stl_vector.h:1379:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_vector.h:1379:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp: In function 'void dd_make_local_top(gmx_domdec_t*, gmx_domdec_zones_t*, int, real (*)[3], real*, const int*, t_forcerec*, real (*)[3], const gmx_mtop_t&, gmx_localtop_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:1028:99: note: parameter passing for argument of type 'std::vector<t_iparams>::const_iterator' changed in GCC 7.1
1028 | iparams_dest.insert(iparams_dest.end(), iparams_src.begin(), iparams_src.end());
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:1028:99: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:53:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:53:
/usr/include/c++/10/bits/stl_vector.h: In function 'void check_assign_interactions_atom(int, int, int, int, int, gmx::ArrayRef<const int>, gmx::ArrayRef<const int>, gmx_bool, int, int, const gmx_domdec_t*, const gmx_domdec_zones_t*, const gmx_molblock_t*, gmx_bool, const int*, gmx_bool, real, t_pbc*, real (*)[3], const t_iparams*, InteractionDefinitions*, int, gmx_bool, int*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/partition.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/utility.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -MF CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o.d -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:254:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
254 | ddSendrecv(dd, d, dddirBackward, gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
255 | gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:254:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:254:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void checkNumberOfBondedInteractions(const gmx::MDLogger&, t_commrec*, int, const gmx_mtop_t*, const gmx_localtop_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3], bool*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3222:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3222 | void checkNumberOfBondedInteractions(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3235:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3235 | dd_print_missing_interactions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3236 | top_local, x, box); // Does not return
| ~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -MF CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o.d -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::scale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
70 | void ScaleCoordinates::Impl::scale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:80:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
80 | void ScaleCoordinates::Impl::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:102:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
102 | void ScaleCoordinates::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:104:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
104 | impl_->scale(coordinates);
| ~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::operator()(gmx::RVec*) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:109:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
109 | impl_->scale({ coordinate, coordinate + 1 });
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
112 | void ScaleCoordinates::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:114:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
114 | impl_->inverseIgnoringZeroScale(coordinates);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::inverseIgnoringZeroScale(gmx::RVec*) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:119:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
119 | impl_->inverseIgnoringZeroScale({ coordinate, coordinate + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::Impl::transform(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:155:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
155 | void TranslateAndScale::Impl::transform(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:176:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
176 | void TranslateAndScale::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:178:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
178 | impl_->transform(coordinates);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::operator()(gmx::RVec*) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:183:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
183 | impl_->transform({ coordinate, coordinate + 1 });
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In constructor 'gmx::AffineTransformation::AffineTransformation(gmx::Matrix3x3ConstSpan, const RVec&)':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:211:1: note: parameter passing for argument of type 'gmx::Matrix3x3ConstSpan' {aka 'gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >'} changed in GCC 7.1
211 | AffineTransformation::AffineTransformation(Matrix3x3ConstSpan matrix, const RVec& translation) :
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::AffineTransformation::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:217:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
217 | void AffineTransformation::operator()(ArrayRef<RVec> vectors) const
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::AffineTransformation::operator()(gmx::RVec*) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:228:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
228 | (*this)({ vector, vector + 1 });
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2105:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2105 | ddSendrecv<gmx::RVec>(dd, dim_ind, dddirBackward, work.positionBuffer, rvecBufferRef);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2105:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2105:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -MF CMakeFiles/libgromacs.dir/math/do_fit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -MF CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o.d -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t&, const t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, gmx::ForceBuffers*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx::VirtualSitesHandler*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2867:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2867 | set_ddbox(*dd, true, DDMASTER(dd) ? state_global->box : nullptr, true, xGlobal, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2908:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2908 | set_ddbox(*dd, bMasterState, state_local->box, true, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2929:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2929 | set_ddbox(*dd, bMasterState, state_local->box, bNStGlobalComm, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2947:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2947 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2948 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), state_local->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2947:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2971:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2971 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2972 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2973 | state_local->x);
| ~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2971:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3006:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3006 | nbnxn_put_on_grid(fr->nbv.get(), state_local->box, 0, comm->zones.size[0].bb_x0,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3007 | comm->zones.size[0].bb_x1, comm->updateGroupsCog.get(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3008 | { 0, dd->ncg_home }, comm->zones.dens_zone0, fr->cginfo, state_local->x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3009 | ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/functions.cpp.o -MF CMakeFiles/libgromacs.dir/math/functions.cpp.o.d -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -MF CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o.d -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/matrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/matrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -MF CMakeFiles/libgromacs.dir/math/neldermead.cpp.o.d -o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/neldermead.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/optimization.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/matrix.cpp: In function 'gmx::Matrix3x3 gmx::transpose(gmx::Matrix3x3ConstSpan)':
/<<PKGBUILDDIR>>/src/gromacs/math/matrix.cpp:50:11: note: parameter passing for argument of type 'gmx::Matrix3x3ConstSpan' {aka 'gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >'} changed in GCC 7.1
50 | Matrix3x3 transpose(Matrix3x3ConstSpan matrixView)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/matrix.cpp: In function 'void gmx::matrixVectorMultiply(gmx::Matrix3x3ConstSpan, gmx::RVec*)':
/<<PKGBUILDDIR>>/src/gromacs/math/matrix.cpp:58:6: note: parameter passing for argument of type 'gmx::Matrix3x3ConstSpan' {aka 'gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >'} changed in GCC 7.1
58 | void matrixVectorMultiply(Matrix3x3ConstSpan matrix, RVec* v)
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/units.cpp.o -MF CMakeFiles/libgromacs.dir/math/units.cpp.o.d -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/optimization.cpp: In function 'gmx::OptimisationResult gmx::nelderMead(const std::function<double(gmx::ArrayRef<const double>)>&, gmx::ArrayRef<const double>, real, int)':
/<<PKGBUILDDIR>>/src/gromacs/math/optimization.cpp:51:20: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
51 | OptimisationResult nelderMead(const std::function<real(ArrayRef<const real>)>& functionToMinimize,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/neldermead.cpp: In constructor 'gmx::NelderMeadSimplex::NelderMeadSimplex(const std::function<double(gmx::ArrayRef<const double>)>&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/math/neldermead.cpp:100:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
100 | NelderMeadSimplex::NelderMeadSimplex(const std::function<real(ArrayRef<const real>)>& f,
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/energyhistory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcebuffers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcebuffers.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcebuffers.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcebuffers.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcebuffers.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::ForceBuffers::resize(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::ForceBuffers::ForceBuffers(bool, gmx::PinningPolicy)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::ForceBuffers::ForceBuffers()':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -Wno-class-memaccess -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/energyhistory.cpp:43:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h: In member function 'std::enable_if_t<gmx::IsSerializableType<T>::value, void> gmx::CheckpointData<gmx::CheckpointDataOperation::Read>::arrayRef(const string&, gmx::ArrayRef<T>) const [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h:442:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
442 | ReadCheckpointData::arrayRef(const std::string& key, ArrayRef<T> values) const
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/interaction_const.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/multipletimestepping.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::index))[3]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:270:7: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
270 | rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n)
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'void printLambdaStateToLog(FILE*, gmx::ArrayRef<double>, bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:344:6: note: parameter passing for argument of type 'const gmx::ArrayRef<double>' changed in GCC 7.1
344 | void printLambdaStateToLog(FILE* fplog, const gmx::ArrayRef<real> lambda, const bool isInitialOutput)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'void initialize_lambdas(FILE*, const t_inputrec&, bool, int*, gmx::ArrayRef<double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:357:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
357 | void initialize_lambdas(FILE* fplog, const t_inputrec& ir, bool isMaster, int* fep_state, gmx::ArrayRef<real> lambda)
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:407:26: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
407 | printLambdaStateToLog(fplog, lambda, isInitialOutput);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:63:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h: In member function 'std::enable_if_t<gmx::IsSerializableType<T>::value, void> gmx::CheckpointData<gmx::CheckpointDataOperation::Read>::arrayRef(const string&, gmx::ArrayRef<T>) const [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h:442:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
442 | ReadCheckpointData::arrayRef(const std::string& key, ArrayRef<T> values) const
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:41:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:41:
/usr/include/c++/10/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:41:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:41:
/usr/include/c++/10/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp: In function 'void gmx::shiftAtoms(const RVec&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp:124:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
124 | void shiftAtoms(const RVec& shift, ArrayRef<RVec> x)
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp: In function 'void gmx::placeCoordinatesWithCOMInBox(const PbcType&, gmx::UnitCellType, gmx::CenteringType, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, const gmx_mtop_t&, gmx::COMShiftType)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
129 | void placeCoordinatesWithCOMInBox(const PbcType& pbcType,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp:86:42: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
86 | put_atoms_in_compact_unitcell(pbcType, static_cast<int>(centerType), box, comArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp:86:42: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp:163:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
163 | shiftAtoms(shift, coords);
| ~~~~~~~~~~^~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(PbcType, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1388:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1388 | void put_atoms_in_box(PbcType pbcType, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box_omp(PbcType, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1448:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1448 | void put_atoms_in_box_omp(PbcType pbcType, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_unused int nth)
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1464:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1464 | void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(PbcType, int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1521:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1521 | void put_atoms_in_compact_unitcell(PbcType pbcType, int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1521:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_molecule_com_in_box(int, int, t_block*, int, t_atom*, PbcType, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
289 | put_atoms_in_compact_unitcell(pbcType, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_residue_com_in_box(int, int, int, t_atom*, PbcType, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:347:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
347 | put_atoms_in_compact_unitcell(pbcType, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:347:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -MF CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:368:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
368 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -MF CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -MF CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atoms.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BaseEntry}; _Tp = BaseEntry; _Alloc = std::allocator<BaseEntry>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BaseEntry>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void readProperty(AtomProperty*, ResidueType*, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BaseEntry*, std::vector<BaseEntry> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -MF CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -MF CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -MF CMakeFiles/libgromacs.dir/topology/invblock.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -MF CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -MF CMakeFiles/libgromacs.dir/topology/symtab.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topology.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topology.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topsort.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -MF CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o.d -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/output.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/output.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator<swap_group>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<swap_group>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 't_swap* init_swapcoords(FILE*, const t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const gmx::MdrunOptions&, gmx::StartingBehavior)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pull.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.h:54,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator<edpar>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::unique_ptr<gmx::EssentialDynamics> ed_open(int, ObservablesHistory*, const char*, const char*, gmx::StartingBehavior, const gmx_output_env_t*, const t_commrec*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef<const gmx::BasicVector<double> >, const t_pbc&, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:944:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
944 | bool pullCheckPbcWithinGroup(const pull_t& pull,
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:944:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
2297 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/simd/support.cpp.o -MF CMakeFiles/libgromacs.dir/simd/support.cpp.o.d -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/anadih.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/angle_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/binsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/cmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dens_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dlist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/eigio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/fitahx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_anaeig.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_analyze.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bundle.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In function 'int gmx_awh(int, char**)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_chi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_confrms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_covar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_current.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_density.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densmap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dielectric.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dipoles.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_disre.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dos.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_mapping&}; _Tp = t_mapping; _Alloc = std::allocator<t_mapping>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_mapping>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'int strip_dssp(FILE*, int, const gmx_bool*, real, real*, FILE*, t_matrix*, int*, const gmx_output_env_t*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In function 'void prune_ss_legend(t_matrix*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dyecoupl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_enemat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_gyrate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_h2order.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hbond.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helixorient.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hydorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_lie.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_make_edi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mdmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmeig.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In constructor 't_corr::t_corr(int, int, int, real, int, gmx_bool, gmx_bool, real, const t_topology*, real, real)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmens.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_order.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'int gmx_nmtraj(int, char**)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp:44:
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_polystat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_potential.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_principal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rama.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotacf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saltbr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sans.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saxs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sham.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sigeps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sorient.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spatial.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_tcaf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_vanhove.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_velacc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wham.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wheel.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/hxprops.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void rainbow_map(gmx_bool, gmx::ArrayRef<t_mapping>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1329:13: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1329 | static void rainbow_map(gmx_bool bBlue, gmx::ArrayRef<t_mapping> map)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void leg_continuous(t_psdata*, real, real, real, const string&, real, char*, gmx::ArrayRef<const t_mapping>, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:250:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
250 | static void leg_continuous(t_psdata* ps,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void ps_mat(const char*, gmx::ArrayRef<t_matrix>, gmx::ArrayRef<t_matrix>, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, int, real, real, real, const char*, const char*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1034:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
1034 | leg_continuous(&out, x0 + w / 2, w / 2, DDD, legend, psr->legfontsize, psr->legfont,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1035 | leg_map, mapoffset);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1034:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
317 | leg_continuous(ps, xx1, x1, y0, label1, fontsize, font, map1, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:318:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
318 | leg_continuous(ps, xx2, x2, y0, label2, fontsize, font, map2, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:318:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nrama.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'int gmx_xpm2ps(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1377:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1377 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1377:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1377 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nsfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/powerspect.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/pp2shift.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/princ.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/sfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcZeroPointEnergy(gmx::ArrayRef<const double>, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:53:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
53 | double calcZeroPointEnergy(gmx::ArrayRef<const real> eigval, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalInternalEnergy(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:66:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
66 | double calcVibrationalInternalEnergy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalHeatCapacity(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:93:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
93 | double calcVibrationalHeatCapacity(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcQuasiHarmonicEntropy(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:158:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
158 | double calcQuasiHarmonicEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool bLinear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcSchlitterEntropy(gmx::ArrayRef<const double>, real, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:185:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
185 | double calcSchlitterEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool bLinear)
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/calch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_param(InteractionsOfType*, int, int, gmx::ArrayRef<const double>, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:56:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
56 | void add_param(InteractionsOfType* ps, int ai, int aj, gmx::ArrayRef<const real> c, const char* s)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:65:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
65 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm, s ? s : ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:65:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite4_atoms(InteractionsOfType*, int, int, int, int, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:102:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
102 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:102:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite3_atoms(InteractionsOfType*, int, int, int, int, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:91:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
91 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:91:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_cmap_param(InteractionsOfType*, int, int, int, int, int, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:71:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
71 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}, s ? s : ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:71:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite2_param(InteractionsOfType*, int, int, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:78:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
78 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:78:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite3_param(InteractionsOfType*, int, int, int, int, real, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:85:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
85 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:85:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/fflibutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In function 'void enter_function(const InteractionsOfType*, t_functype, int, real, gmx_ffparams_t*, InteractionList*, bool, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void enter_function(const InteractionsOfType*, t_functype, int, real, gmx_ffparams_t*, InteractionList*, bool, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<InteractionOfType, int>}; _Tp = std::pair<InteractionOfType, int>; _Alloc = std::allocator<std::pair<InteractionOfType, int> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<InteractionOfType, int> >::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp: In function 'std::vector<InteractionOfType> clean_dih(gmx::ArrayRef<const InteractionOfType>, gmx::ArrayRef<const InteractionOfType>, t_atoms*, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:233:39: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
233 | static std::vector<InteractionOfType> clean_dih(gmx::ArrayRef<const InteractionOfType> dih,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:233:39: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<InteractionOfType, int>*, std::vector<std::pair<InteractionOfType, int> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<InteractionOfType, int>*, std::vector<std::pair<InteractionOfType, int> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genconf.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1886:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1886 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1886:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Distance = int; _Tp = InteractionOfType; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_6ring(t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, real, real, real, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/stl_heap.h:424:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
424 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_his(t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp: In function 'void gen_pad(t_atoms*, gmx::ArrayRef<const PreprocessResidue>, gmx::ArrayRef<InteractionsOfType>, t_excls*, gmx::ArrayRef<MoleculePatchDatabase>, bool, gmx::ArrayRef<const int>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:674:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
674 | ang.push_back(InteractionOfType(atomNumbers, {}, name));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:674:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:725:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
725 | dih.push_back(InteractionOfType(atomNumbers, {}, name));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:725:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:735:51: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
735 | dih.push_back(InteractionOfType(atoms, {}, ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:735:51: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:754:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
754 | pai.push_back(InteractionOfType(atoms, {}, ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:754:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:822:35: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
822 | ang.push_back(InteractionOfType(atomNumbers, {}, bondeds.s));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:822:35: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:875:35: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
875 | dih.push_back(InteractionOfType(atomNumbers, {}, bondeds.s));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:875:35: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1982 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1982 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1982 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:372:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
372 | improper.emplace_back(InteractionOfType(ai, {}, bondeds.s));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:372:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:916:24: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
916 | dih = clean_dih(dih, improper, atoms, rtpFFDB[0].bKeepAllGeneratedDihedrals,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
917 | rtpFFDB[0].bRemoveDihedralIfWithImproper);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:916:24: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:916:24: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_tyr(PreprocessingAtomTypes*, std::vector<gmx::BasicVector<double> >*, t_atom**, char****, int**, int**, int**, t_symtab*, int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int**, t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, int, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_trp(PreprocessingAtomTypes*, std::vector<gmx::BasicVector<double> >*, t_atom**, char****, int**, int**, int**, t_symtab*, int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int**, t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, int, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genion.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MoleculePatch&}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function 'void expand_hackblocks_one(const MoleculePatchDatabase&, std::string, std::vector<MoleculePatch>*, bool, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'void do_vsites(gmx::ArrayRef<const PreprocessResidue>, PreprocessingAtomTypes*, t_atoms*, t_symtab*, std::vector<gmx::BasicVector<double> >*, gmx::ArrayRef<InteractionsOfType>, int**, int**, real, bool, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:2248:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2248 | *parm = InteractionOfType(newAtomNumber, parm->forceParam(), parm->interactionTypeName());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:2248:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genrestr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gmxcpp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&, char**, const InteractionOfType&, int&, int&}; _Tp = AtomTypeData; _Alloc = std::allocator<AtomTypeData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AtomTypeData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'int PreprocessingAtomTypes::addType(t_symtab*, const t_atom&, const string&, const InteractionOfType&, int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/c++/10/bits/c++allocator.h:33,
from /usr/include/c++/10/bits/allocator.h:46,
from /usr/include/c++/10/string:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:40:
/usr/include/c++/10/ext/new_allocator.h:156:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
156 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/ext/new_allocator.h:156:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const AtomTypeData&}; _Tp = AtomTypeData; _Alloc = std::allocator<AtomTypeData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AtomTypeData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/c++/10/bits/c++allocator.h:33,
from /usr/include/c++/10/bits/allocator.h:46,
from /usr/include/c++/10/string:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:40:
/usr/include/c++/10/ext/new_allocator.h: In member function 'void PreprocessingAtomTypes::renumberTypes(gmx::ArrayRef<InteractionsOfType>, gmx_mtop_t*, int*, bool)':
/usr/include/c++/10/ext/new_allocator.h:156:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
156 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/ext/new_allocator.h:156:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:46:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:46:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:41:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:41:
/usr/include/c++/10/bits/stl_vector.h: In function 'void copyPreprocessResidues(const PreprocessResidue&, PreprocessResidue*, t_symtab*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp: In constructor 'InteractionOfType::InteractionOfType(gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, const string&)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp:114:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
114 | InteractionOfType::InteractionOfType(gmx::ArrayRef<const int> atoms,
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:41:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MoleculePatch&}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:41:
/usr/include/c++/10/bits/stl_vector.h: In function 'void mergeAtomModifications(const MoleculePatchDatabase&, MoleculePatchDatabase*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hizzie.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp:41:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {MoleculePatch}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void read_h_db_file(const char*, std::vector<MoleculePatchDatabase>*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp: In function 'void insert_mols(int, int, int, real, real, t_atoms*, t_symtab*, std::vector<gmx::BasicVector<double> >*, const std::set<int>&, const t_atoms&, gmx::ArrayRef<gmx::BasicVector<double> >, PbcType, real (*)[3], const string&, const real*, RotationType)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp:171:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
171 | static void insert_mols(int nmol_insrt,
| ^~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:38:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<double> makeExclusionDistances(const t_atoms*, AtomProperties*, real, real)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp: In function 'int nm2type(int, t_nm2type*, t_symtab*, t_atoms*, PreprocessingAtomTypes*, int*, InteractionsOfType*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp:343:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
343 | k = atype->addType(tab, atoms->atom[i], type, InteractionOfType({}, {}),
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp:343:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp: In member function 'virtual int gmx::{anonymous}::InsertMolecules::run()':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp:589:16: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
589 | insert_mols(nmolIns_, nmolTry_, seed_, defaultDistance_, scaleFactor_, &atoms, &top_.symtab,
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
590 | &x_, removableAtoms, atomsInserted, xInserted, pbcTypeForOutput, box_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
591 | positionFile_, deltaR_, enumRot_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pgutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readir.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void add_atom_to_restp(PreprocessResidue*, t_symtab*, int, const MoleculePatch*)':
/usr/include/c++/10/bits/vector.tcc:161:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
161 | _M_realloc_insert(begin() + (__position - cbegin()), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp: In function 'void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue>, gmx::ArrayRef<MoleculePatchDatabase>, t_atoms*, t_symtab*, gmx::ArrayRef<gmx::BasicVector<double> >, bool, const gmx::MDLogger&)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:1335:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1335 | void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue> usedPpResidues,
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void {anonymous}::sort_pdbatoms(gmx::ArrayRef<const PreprocessResidue>, int, t_atoms**, t_atoms**, std::vector<gmx::BasicVector<double> >*, t_blocka*, char***)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Distance = int; _Tp = InteractionOfType; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/10/bits/stl_heap.h:424:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
424 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual int gmx::{anonymous}::pdb2gmx::run()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:2399:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2399 | match_atomnames_with_rtp(restp_chain, hb_chain, pdba, &symtab, x, bVerbose_, logger);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp: In function 'void pdb2top(FILE*, const char*, const char*, t_atoms*, std::vector<gmx::BasicVector<double> >*, PreprocessingAtomTypes*, t_symtab*, gmx::ArrayRef<const PreprocessResidue>, gmx::ArrayRef<PreprocessResidue>, gmx::ArrayRef<MoleculePatchDatabase>, bool, bool, bool, const char*, real, gmx::ArrayRef<const DisulfideBond>, real, real, bool, bool, bool, bool, bool, gmx::ArrayRef<const int>, const gmx::MDLogger&)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:808:26: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
808 | add_param(psb, ai, aj, {}, patch.s.c_str());
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:808:26: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:822:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
822 | add_param(psb, i, i + 1, {}, nullptr); /* C-O */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:822:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:823:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
823 | add_param(psb, i, i + 2, {}, nullptr); /* C-OA */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:823:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:824:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
824 | add_param(psb, i + 2, i + 3, {}, nullptr); /* OA-H */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:824:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:829:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
829 | add_param(psb, i, i + k + 1, {}, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:829:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:749:18: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
749 | add_param(ps, ai, aj, {}, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:749:18: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function 'void process_pull_groups(gmx::ArrayRef<t_pull_group>, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, const t_blocka*, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:453:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'gmx::index' {aka 'int'} [-Wformat=]
453 | "Number of weights (%ld) for pull group %d '%s' does not match the number of "
| ~~^
| |
| long int
| %d
454 | "atoms (%ld)",
455 | gmx::ssize(pullGroup.weight), g, pullGroupNames[g].c_str(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| gmx::index {aka int}
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:454:33: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'gmx::index' {aka 'int'} [-Wformat=]
454 | "atoms (%ld)",
| ~~^
| |
| long int
| %d
455 | gmx::ssize(pullGroup.weight), g, pullGroupNames[g].c_str(),
456 | gmx::ssize(pullGroup.ind));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| gmx::index {aka int}
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function 'void checkPullCoords(gmx::ArrayRef<const t_pull_group>, gmx::ArrayRef<const t_pull_coord>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:484:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_pull_coord>' changed in GCC 7.1
484 | void checkPullCoords(gmx::ArrayRef<const t_pull_group> pullGroups, gmx::ArrayRef<const t_pull_coord> pullCoords)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function 'pull_t* set_pull_init(t_inputrec*, const gmx_mtop_t*, real (*)[3], real (*)[3], real, warninp_t)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:546:53: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
546 | bool groupObeysPbc = pullCheckPbcWithinGroup(
| ~~~~~~~~~~~~~~~~~~~~~~~^
547 | *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
548 | pbc, g, c_pullGroupSmallGroupThreshold);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:577:52: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
577 | groupObeysPbc = pullCheckPbcWithinGroup(
| ~~~~~~~~~~~~~~~~~~~~~~~^
578 | *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
579 | pbc, g, c_pullGroupPbcMargin);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = t_pull_coord; _Alloc = std::allocator<t_pull_coord>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_pull_coord>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<std::__cxx11::basic_string<char> > read_pullparams(std::vector<t_inpfile>*, pull_params_t*, warninp_t)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:45:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_pull_coord*, std::vector<t_pull_coord> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readrot.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::BenchmarkSystem::BenchmarkSystem(int, const string&)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SpecialBond&}; _Tp = SpecialBond; _Alloc = std::allocator<SpecialBond>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<SpecialBond>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<SpecialBond> generateSpecialBonds()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SpecialBond*, std::vector<SpecialBond> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {MoleculePatch}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'void read_ter_db_file(const char*, std::vector<MoleculePatchDatabase>*, PreprocessingAtomTypes*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'int gmx_solvate(int, char**)':
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
1665 | _M_range_insert(__pos, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
1666 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
1665 | _M_range_insert(__pos, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
1666 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp: In function 'void convert_harmonics(gmx::ArrayRef<MoleculeInformation>, PreprocessingAtomTypes*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:232:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
232 | InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:232:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:49:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp: In function 'PreprocessingAtomTypes read_atype(const char*, t_symtab*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:95:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
95 | at.addType(tab, *a, name, InteractionOfType({}, {}), 0, 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:95:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp: In function 'void make_shake(gmx::ArrayRef<InteractionsOfType>, t_atoms*, int, const gmx::MDLogger&)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:185:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
185 | InteractionOfType(atomNumbers, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:185:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:217:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
217 | add_param_to_list(&(plist[F_CONSTR]), InteractionOfType(atomNumbers, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:217:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp: In function 'char** read_topol(const char*, const char*, const char*, const char*, t_symtab*, PreprocessingAtomTypes*, std::vector<MoleculeInformation>*, std::unique_ptr<MoleculeInformation>*, gmx::ArrayRef<InteractionsOfType>, int*, double*, t_gromppopts*, real*, std::vector<gmx_molblock_t>*, bool*, bool, bool, bool, warninp*, const gmx::MDLogger&)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:137:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
137 | pairs->interactionTypes.emplace_back(InteractionOfType(atomNumbers, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:137:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void readResidueDatabase(const string&, std::vector<PreprocessResidue>*, PreprocessingAtomTypes*, t_symtab*, const gmx::MDLogger&, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void generate_LJCpairsNB(MoleculeInformation*, int, InteractionsOfType*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2657:71: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2657 | add_param_to_list(&mol->interactions[F_LJC_PAIRS_NB], InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2657:71: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_at(t_symtab*, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, int, t_nbparam***, t_nbparam***, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:542:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
542 | InteractionOfType interactionType({}, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:542:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp: In function 'void print_bondeds(FILE*, int, Directive, int, int, gmx::ArrayRef<const InteractionsOfType>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:341:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
341 | atype.addType(&stab, *a, buf, InteractionOfType({}, {}), 0, 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:341:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void add_param_to_list(InteractionsOfType*, const InteractionOfType&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bond(Directive, gmx::ArrayRef<InteractionsOfType>, gmx::ArrayRef<InteractionsOfType>, t_atoms*, PreprocessingAtomTypes*, char*, bool, bool, real, bool, bool*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1985:50: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1985 | InteractionOfType param(atoms, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1985:50: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_cmap(Directive, gmx::ArrayRef<InteractionsOfType>, gmx::ArrayRef<InteractionsOfType>, t_atoms*, PreprocessingAtomTypes*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2337:64: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2337 | InteractionOfType param(atoms, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2337:64: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_vsitesn(Directive, gmx::ArrayRef<InteractionsOfType>, t_atoms*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2444:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2444 | add_param_to_list(&bond[ftype], InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2444:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'int add_atomtype_decoupled(t_symtab*, PreprocessingAtomTypes*, t_nbparam***, t_nbparam***)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2575:49: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2575 | nr = at->addType(symtab, atom, "decoupled", InteractionOfType({}, forceParam, ""), -1, 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2575:49: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/xlate.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void generate_nbparams(int, int, InteractionsOfType*, PreprocessingAtomTypes*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:104:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:104:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:128:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
128 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:128:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:152:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
152 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:152:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:185:65: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
185 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:185:65: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bondtype(InteractionsOfType*, const InteractionOfType&, int, int, bool, const char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:712:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
712 | InteractionOfType(b.atoms(), b.forceParam(), b.interactionTypeName()));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:712:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:731:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
731 | bt->interactionTypes.emplace_back(InteractionOfType(atoms, forceParam, b.interactionTypeName()));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:731:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bt(Directive, gmx::ArrayRef<InteractionsOfType>, int, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:852:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
852 | push_bondtype(&(bt[ftype]), InteractionOfType(atomTypes, forceParam), nral, ftype, FALSE, line, wi);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:852:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_dihedraltype(Directive, gmx::ArrayRef<InteractionsOfType>, PreprocessingBondAtomType*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1020:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1020 | push_bondtype(&(bt[ftype]), InteractionOfType(atoms, forceParam), 4, ftype, bAllowRepeat, line, wi);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1020:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'void push_cmaptype(Directive, gmx::ArrayRef<InteractionsOfType>, int, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, warninp*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1287:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | push_bondtype(&(bt[ftype]), InteractionOfType(atomTypes, forceParam), nral, ftype, FALSE, line, wi);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1287:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp: In function 'bool calc_vsite3out_param(PreprocessingAtomTypes*, InteractionOfType*, t_atoms*, gmx::ArrayRef<const VsiteBondedInteraction>, gmx::ArrayRef<const VsiteBondedInteraction>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:544:13: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
544 | static bool calc_vsite3out_param(PreprocessingAtomTypes* atypes,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:544:13: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'void convert_pairs_to_pairsQ(gmx::ArrayRef<InteractionsOfType>, real, t_atoms*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2607:31: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2607 | paramnew.emplace_back(InteractionOfType(param.atoms(), forceParam, ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2607:31: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp: In function 'void lo_set_force_const(InteractionsOfType*, real*, int, bool, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | param = InteractionOfType(param.atoms(), forceParam);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VsiteBondedInteraction}; _Tp = VsiteBondedInteraction; _Alloc = std::allocator<VsiteBondedInteraction>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VsiteBondedInteraction>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'void enter_bonded(int, std::vector<VsiteBondedInteraction>*, const InteractionOfType&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VsiteBondedInteraction*, std::vector<VsiteBondedInteraction> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp: In function 'int gmx_x2top(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:136:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
136 | add_param_to_list(bond, InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:136:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | param = InteractionOfType(param.atoms(), forceParam);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp: In function 'int set_vsites(bool, t_atoms*, PreprocessingAtomTypes*, gmx::ArrayRef<InteractionsOfType>, const gmx::MDLogger&)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:849:58: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
849 | bERROR = calc_vsite3out_param(atypes, ¶m, atoms, allVsiteBondeds.bonds,
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
850 | allVsiteBondeds.angles);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:849:58: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:849:58: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/crosscorr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/expfit.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void low_do_four_core(int, real*, real*, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void low_do_autocorr(const char*, const gmx_output_env_t*, const char*, int, int, int, real**, real, long unsigned int, int, gmx_bool, gmx_bool, gmx_bool, real, real, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/gmx_lmcurve.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/integrate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/polynomials.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -MF CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o.d -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/statistics/statistics.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/abstractdata.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'void clean_vsite_bondeds(gmx::ArrayRef<InteractionsOfType>, int, bool, const gmx::MDLogger&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:46:
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function '_Z16many_auto_correlPSt6vectorIS_IdSaIdEESaIS1_EE._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'int many_auto_correl(std::vector<std::vector<double> >*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataproxy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::AbstractAnalysisArrayData::AbstractAnalysisArrayData()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/average.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/frameaverager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/histogram.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/lifetime.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::AnalysisDataDisplacementModule::frameFinished(const gmx::AnalysisDataFrameHeader&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/plot.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::AnalysisDataValue&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::internal::AnalysisDataStorageFrameData::addPointSet(int, int, gmx::ArrayRef<const gmx::AnalysisDataValue>)':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:584:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
584 | void AnalysisDataStorageFrameData::addPointSet(int dataSetIndex,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::AnalysisDataStorageFrame::finishPointSet()':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:715:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
715 | data_->addPointSet(currentDataSet_, firstColumn,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
716 | makeConstArrayRef(values_).subArray(begin, end - begin));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:715:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/coordinatefile.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/outputselector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setforces.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setprecision.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setvelocities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:45:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp:48:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp:48:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::analysismodules::{anonymous}::Sasa::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/check.cpp.o -MF CMakeFiles/libgromacs.dir/tools/check.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/check.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -MF CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/convert_tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/dump.cpp.o -MF CMakeFiles/libgromacs.dir/tools/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/eneconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/make_ndx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/mk_angndx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -MF CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/pme_error.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -MF CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjcat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -MF CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tune_pme.cpp
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp: In function 'int gmx_trjconv(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp:1246:66: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1246 | put_atoms_in_compact_unitcell(pbcType, ecenter, fr.box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
1247 | positionsArrayRef);
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp:1246:66: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp:111:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
111 | void BoxDeformation::apply(ArrayRef<RVec> x, matrix box, int64_t step)
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:41:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:41:
/usr/include/c++/10/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(MPI_Comm, bool, bool, t_state*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator<VerletbufAtomtype>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VerletbufAtomtype>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<VerletbufAtomtype> getVerletBufferAtomtypes(const gmx_mtop_t&, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*, const real*, int, double*, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp:52:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
52 | void calc_mu(int start,
| ^~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const gmx::ListOfLists<int>&, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, gmx::ArrayRef<int>, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
60 | static void constr_recur(const ListOfLists<int>& at2con,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const gmx::ListOfLists<int>&, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, gmx::ArrayRef<int>, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function '_ZN3gmx11Constraints4Impl5applyEbbxidNS_19ArrayRefWithPaddingINS_11BasicVectorIdEEEES5_NS_8ArrayRefIS4_EEPA3_KddPdS5_bPA3_dNS_18ConstraintVariableE._omp_fn.1':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:575:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
575 | settle_proj(*settled, econq, end_th - start_th,
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
576 | settle.iatoms.data() + start_th * (1 + NRAL(F_SETTLE)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
577 | pbc_null, x.unpaddedArrayRef(), xprime.unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
578 | min_proj, calcvir_atom_end,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
579 | th == 0 ? constraintsVirial : threadConstraintsVirial[th]);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:575:40: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:575:40: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 'int gmx::countFlexibleConstraints(gmx::ArrayRef<const InteractionList>, gmx::ArrayRef<const t_iparams>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:869:5: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
869 | int countFlexibleConstraints(ArrayRef<const InteractionList> ilist, ArrayRef<const t_iparams> iparams)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In member function 'bool gmx::Constraints::Impl::apply(bool, bool, int64_t, int, real, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, const real (*)[3], real, real*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, bool, real (*)[3], gmx::ConstraintVariable)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:363:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
363 | bool Constraints::Impl::apply(bool bLog,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:464:30: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
464 | dd_move_x_constraints(cr->dd, box, x.unpaddedArrayRef(), xprime.unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
465 | econq == ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:479:30: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
479 | bOK = constrain_lincs(bLog || bEner, ir, step, lincsd, inverseMasses_, cr, ms, x, xprime,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
480 | min_proj, box, pbc_null, hasMassPerturbedAtoms_, lambda, dvdlambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
481 | invdt, v.unpaddedArrayRef(), computeVirial, constraintsVirial, econq,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
482 | nrnb, maxwarn, &warncount_lincs);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:479:30: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:496:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
496 | bOK = constrain_shake(log, shaked.get(), inverseMasses_, *idef, ir, x.unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
497 | xprime.unpaddedArrayRef(), min_proj, pbc_null, nrnb, lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
498 | dvdlambda, invdt, v.unpaddedArrayRef(), computeVirial,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
499 | constraintsVirial, maxwarn < INT_MAX, econq);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:496:30: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:496:30: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:496:30: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In member function 'bool gmx::Constraints::apply(bool, bool, int64_t, int, real, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, const real (*)[3], real, real*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, bool, real (*)[3], gmx::ConstraintVariable)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:342:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
342 | bool Constraints::apply(bool bLog,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:358:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
358 | return impl_->apply(bLog, bEner, step, delta_step, step_scaling, std::move(x),
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
359 | std::move(xprime), min_proj, box, lambda, dvdlambda, std::move(v),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
360 | computeVirial, constraintsVirial, econq);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 'void gmx::constrain_velocities(gmx::Constraints*, bool, bool, int64_t, t_state*, real*, gmx_bool, real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:1277:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1277 | constr->apply(do_log, do_ene, step, 1, 1.0, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1278 | state->v.arrayRefWithPadding(), state->v.arrayRefWithPadding().unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1279 | state->box, state->lambda[efptBONDED], dvdlambda, ArrayRefWithPadding<RVec>(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1280 | computeVirial, constraintsVirial, ConstraintVariable::Velocities);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 'void gmx::constrain_coordinates(gmx::Constraints*, bool, bool, int64_t, t_state*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real*, gmx_bool, real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:1296:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1296 | constr->apply(do_log, do_ene, step, 1, 1.0, state->x.arrayRefWithPadding(), std::move(xp),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1297 | ArrayRef<RVec>(), state->box, state->lambda[efptBONDED], dvdlambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1298 | state->v.arrayRefWithPadding(), computeVirial, constraintsVirial,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1299 | ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 'gmx::ListOfLists<int> gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:860:18: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
860 | ListOfLists<int> make_at2con(const gmx_moltype_t& moltype,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 'gmx::ListOfLists<int> gmx::make_at2con(int, gmx::ArrayRef<const InteractionList>, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:852:18: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
852 | ListOfLists<int> make_at2con(int numAtoms,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:108:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
108 | DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp: In function 'void add_ebin_indexed(t_ebin*, int, gmx::ArrayRef<bool>, gmx::ArrayRef<const double>, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp:199:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
199 | void add_ebin_indexed(t_ebin* eb,
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, real, const std::vector<bool>&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:1268:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1268 | void andersen_tcoupl(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:1268:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::do_constrain_first(FILE*, gmx::Constraints*, const t_inputrec*, int, int, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, const real (*)[3], real)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:1218:18: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1218 | constr->apply(needsLogging, computeEnergy, step, 0, 1.0, x, x, {}, box, lambda, &dvdl_dum, {},
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1219 | computeVirial, nullptr, gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:1224:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1224 | constr->apply(needsLogging, computeEnergy, step, 0, 1.0, x, v, v.unpaddedArrayRef(), box, lambda,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1225 | &dvdl_dum, {}, computeVirial, nullptr, gmx::ConstraintVariable::Velocities);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:1251:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1251 | constr->apply(needsLogging, computeEnergy, step, -1, 1.0, x, savex.arrayRefWithPadding(),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1252 | {}, box, lambda, &dvdl_dum, v, computeVirial, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1253 | gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'gmx_bool update_randomize_velocities(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, const gmx::Update*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:293:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
293 | extern gmx_bool update_randomize_velocities(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:321:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
321 | andersen_tcoupl(ir, step, cr, md, v, rate, upd->getAndersenRandomizeGroup(),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
322 | upd->getBoltzmanFactor());
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:321:24: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::DispersionCorrection(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>, const interaction_const_t&, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:518:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
518 | DispersionCorrection::DispersionCorrection(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:528:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
528 | topParams_(mtop, inputrec, useBuckingham, numAtomTypes, nonbondedForceParameters)
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energydrifttracker.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'void update_pcouple_after_coordinates(FILE*, int64_t, const t_inputrec*, const t_mdatoms*, const real (*)[3], const real (*)[3], const real (*)[3], real (*)[3], t_state*, t_nrnb*, gmx::BoxDeformation*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:289:30: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
289 | boxDeformation->apply(localX, state->box, step);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In member function 'void ForeignLambdaTerms::finalizePotentialContributions(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, const t_lambda&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:173:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
173 | void ForeignLambdaTerms::finalizePotentialContributions(gmx::ArrayRef<const double> dvdlLinear,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:173:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function 'void accumulatePotentialEnergies(gmx_enerdata_t*, gmx::ArrayRef<const double>, const t_lambda*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:219:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
219 | void accumulatePotentialEnergies(gmx_enerdata_t* enerd, gmx::ArrayRef<const real> lambda, const t_lambda* fepvals)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:235:65: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
235 | enerd->foreignLambdaTerms.finalizePotentialContributions(enerd->dvdl_lin, lambda, *fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:235:65: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:235:65: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In member function 'void ForeignLambdaTerms::finalizeKineticContributions(gmx::ArrayRef<const double>, double, gmx::ArrayRef<const double>, const t_lambda&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:245:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
245 | void ForeignLambdaTerms::finalizeKineticContributions(gmx::ArrayRef<const real> energyTerms,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:245:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function 'void accumulateKineticLambdaComponents(gmx_enerdata_t*, gmx::ArrayRef<const double>, const t_lambda&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:280:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
280 | void accumulateKineticLambdaComponents(gmx_enerdata_t* enerd,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:296:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
296 | enerd->foreignLambdaTerms.finalizeKineticContributions(enerd->term, enerd->dvdl_lin[efptMASS],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
297 | lambda, fepvals);
| ~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:296:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:296:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp: In function 'void calculateLongRangeNonbondeds(t_forcerec*, const t_inputrec*, const t_commrec*, t_nrnb*, gmx_wallcycle_t, const t_mdatoms*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ForceWithVirial*, gmx_enerdata_t*, const real (*)[3], const real*, const real (*)[3], const gmx::StepWorkload&, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:101:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
101 | void calculateLongRangeNonbondeds(t_forcerec* fr,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:197:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
197 | status = gmx_pme_do(
| ~~~~~~~~~~^
198 | fr->pmedata,
| ~~~~~~~~~~~~
199 | gmx::constArrayRefFromArray(coordinates.data(), md->homenr - fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | forceWithVirial->force_, md->chargeA, md->chargeB, md->sqrt_c6A,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | md->sqrt_c6B, md->sigmaA, md->sigmaB, box, cr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
202 | DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
203 | DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0, nrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
204 | ewaldOutput.vir_q, ewaldOutput.vir_lj, &Vlr_q, &Vlr_lj,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
205 | lambda[efptCOUL], lambda[efptVDW], &ewaldOutput.dvdl[efptCOUL],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
206 | &ewaldOutput.dvdl[efptVDW], stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:197:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:197:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:226:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
226 | gmx_pme_calc_energy(
| ~~~~~~~~~~~~~~~~~~~^
227 | fr->pmedata, coordinates.subArray(md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
228 | gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
229 | &Vlr_q);
| ~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:226:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:226:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/freeenergyparameters.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp: In member function 'void gmx::EnergyOutput::addDataAtEnergyStep(bool, bool, double, real, const gmx_enerdata_t*, const t_lambda*, const t_expanded*, const real (*)[3], gmx::PTCouplingArrays, int, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const gmx_ekindata_t*, const real*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp:891:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
891 | add_ebin_indexed(ebin_, ie_, gmx::ArrayRef<bool>(bEner_), enerd->term, bSum);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gpuforcereduction_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:49:
/usr/include/c++/10/bits/unique_ptr.h: In function 'void init_forcerec(FILE*, const gmx::MDLogger&, t_forcerec*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, real (*)[3], const char*, const char*, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, real)':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function 'void gmx::lincs_update_atoms(gmx::Lincs*, int, real, gmx::ArrayRef<const double>, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*, real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:445:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
445 | static void lincs_update_atoms(Lincs* li,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:445:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp: In function 'void compute_globals(gmx_global_stat*, t_commrec*, const t_inputrec*, t_forcerec*, gmx_ekindata_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3], const t_mdatoms*, t_nrnb*, t_vcm*, gmx_wallcycle_t, gmx_enerdata_t*, real (*)[3], real (*)[3], real (*)[3], real (*)[3], gmx::Constraints*, gmx::SimulationSignaller*, const real (*)[3], int*, gmx_bool*, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:297:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
297 | void compute_globals(gmx_global_stat* gstat,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:297:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:366:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
366 | calc_vcm_grp(*mdatoms, x, v, vcm);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:366:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:366:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function '_ZN3gmx15constrain_lincsEbRK10t_inputrecxPNS_5LincsEPKdPK9t_commrecPK14gmx_multisim_tNS_19ArrayRefWithPaddingIKNS_11BasicVectorIdEEEENSD_ISF_EENS_8ArrayRefISF_EEPA3_S5_P5t_pbcbdPddSK_bPA3_dNS_18ConstraintVariableEP6t_nrnbiPi._omp_fn.1':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:711:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
711 | lincs_update_atoms(lincsd, th, 1.0, sol, r, (econq != ConstraintVariable::Force) ? invmass : nullptr,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
712 | as_rvec_array(fp.data()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:711:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function '_ZN3gmx15constrain_lincsEbRK10t_inputrecxPNS_5LincsEPKdPK9t_commrecPK14gmx_multisim_tNS_19ArrayRefWithPaddingIKNS_11BasicVectorIdEEEENSD_ISF_EENS_8ArrayRefISF_EEPA3_S5_P5t_pbcbdPddSK_bPA3_dNS_18ConstraintVariableEP6t_nrnbiPi._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1086:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1086 | lincs_update_atoms(lincsd, th, 1.0, mlambda, r, invmass, xp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1107:42: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1107 | dd_move_x_constraints(cr->dd, box, xpPadded.unpaddedArrayRef(), ArrayRef<RVec>(), FALSE);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1148:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1148 | lincs_update_atoms(lincsd, th, 1.0, blc_sol, r, invmass, xp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1155:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1155 | lincs_update_atoms(lincsd, th, invdt, mlambda, r, invmass, v);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function 'bool gmx::constrain_lincs(bool, const t_inputrec&, int64_t, gmx::Lincs*, const real*, const t_commrec*, const gmx_multisim_t*, gmx::ArrayRefWithPadding<const gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, const real (*)[3], t_pbc*, bool, real, real*, real, gmx::ArrayRef<gmx::BasicVector<double> >, bool, real (*)[3], gmx::ConstraintVariable, t_nrnb*, int, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:2259:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2259 | bool constrain_lincs(bool computeRmsd,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:2259:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resizeChargeA(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resizeChargeB(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function 'void gmx::set_lincs(const InteractionDefinitions&, int, const real*, real, bool, const t_commrec*, gmx::Lincs*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1911:94: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
1911 | make_at2con(natoms, idef.il, idef.iparams, flexibleConstraintTreatment(bDynamics));
| ^
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:47:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, int, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::WriteCheckpointDataHolder*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:513:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
513 | void mdoutf_write_to_trajectory_files(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:539:31: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
539 | dd_collect_vec(cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
540 | state_local->cg_gl, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:539:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:545:31: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
545 | dd_collect_vec(cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
546 | state_local->cg_gl, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:545:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:552:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
552 | dd_collect_vec(
| ~~~~~~~~~~~~~~^
553 | cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl, f_local,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
554 | gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(of->f_global), f_local.size()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:552:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'int add_binr(t_bin*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
103 | int add_binr(t_bin* b, gmx::ArrayRef<const real> r)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'void extract_binr(t_bin*, int, gmx::ArrayRef<double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
160 | void extract_binr(t_bin* b, int index, gmx::ArrayRef<real> r)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp: In function 'void gmx::settle_proj(const gmx::SettleData&, gmx::ConstraintVariable, int, const t_iatom*, const t_pbc*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, int, real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp:260:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
260 | void settle_proj(const SettleData& settled,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp:260:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp:260:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp: In function 'void gmx::cshake(const int*, int, int*, int, gmx::ArrayRef<const double>, gmx::ArrayRef<gmx::BasicVector<double> >, const t_pbc*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const double>, real, const real*, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:270:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
270 | void cshake(const int iatom[],
| ^~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:270:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:270:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:270:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:270:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:270:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp: In function 'bool gmx::bshakef(FILE*, gmx::shakedata*, const real*, const InteractionDefinitions&, const t_inputrec&, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, const t_pbc*, t_nrnb*, real, real*, real, gmx::ArrayRef<gmx::BasicVector<double> >, bool, real (*)[3], bool, gmx::ConstraintVariable)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:655:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
655 | static bool bshakef(FILE* log,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:655:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:655:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:505:19: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
505 | cshake(iatom, ncon, &nit, maxnit, constraint_distance_squared, prime, pbc, rij,
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
506 | half_of_reduced_mass, omega, invmass, distance_squared_tolerance,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
507 | scaled_lagrange_multiplier, &error);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:505:19: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:505:19: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:505:19: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:505:19: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:505:19: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp: In function 'bool gmx::constrain_shake(FILE*, gmx::shakedata*, const real*, const InteractionDefinitions&, const t_inputrec&, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, const t_pbc*, t_nrnb*, real, real*, real, gmx::ArrayRef<gmx::BasicVector<double> >, bool, real (*)[3], bool, gmx::ConstraintVariable)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:761:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
761 | bool constrain_shake(FILE* log,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:761:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:761:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:761:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:788:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
788 | bOK = bshakef(log, shaked, invmass, idef, ir, x_s, xprime, pbc, nrnb, lambda, dvdlambda,
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
789 | invdt, v, bCalcVir, vir_r_m_dr, bDumpOnError, econq);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:788:26: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:788:26: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:792:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
792 | bOK = bshakef(log, shaked, invmass, idef, ir, x_s, vprime, pbc, nrnb, lambda, dvdlambda,
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
793 | invdt, {}, bCalcVir, vir_r_m_dr, bDumpOnError, econq);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:792:26: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:792:26: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void postProcessForceWithShiftForces(t_nrnb*, gmx_wallcycle_t, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ForceOutputs*, real (*)[3], const t_mdatoms&, const t_forcerec&, gmx::VirtualSitesHandler*, const gmx::StepWorkload&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:282:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
282 | static void postProcessForceWithShiftForces(t_nrnb* nrnb,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:307:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
307 | vsite->spreadForces(x, f, virialHandling, fshift, nullptr, nrnb, box, wcycle);
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:307:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:307:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:307:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void postProcessForces(const t_commrec*, int64_t, t_nrnb*, gmx_wallcycle_t, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ForceOutputs*, real (*)[3], const t_mdatoms*, const t_forcerec*, gmx::VirtualSitesHandler*, const gmx::StepWorkload&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:320:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
320 | static void postProcessForces(const t_commrec* cr,
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:357:32: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
357 | vsite->spreadForces(x, forceWithVirial.force_, virialHandling, {}, virial, nrnb, box, wcycle);
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:357:32: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:357:32: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:357:32: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, gmx::ImdSession*, pull_t*, int64_t, t_nrnb*, gmx_wallcycle_t, const gmx_localtop_t*, const real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ForceBuffersView*, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, gmx::ArrayRef<const double>, t_forcerec*, gmx::MdrunScheduleWorkload*, gmx::VirtualSitesHandler*, real*, double, gmx_edsam*, int, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1125:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1125 | void do_force(FILE* fplog,
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1236:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1236 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1279:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1279 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1306:62: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1306 | fr->wholeMoleculeTransform->updateForAtomPbcJumps(x.unpaddedArrayRef(), box);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1325:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1325 | nbnxn_put_on_grid(nbv, box, 0, vzero, box_diag, nullptr, { 0, mdatoms->homenr }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1326 | fr->cginfo, x.unpaddedArrayRef(), 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1332:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1332 | nbnxn_put_on_grid_nonlocal(nbv, domdec_zones(cr->dd), fr->cginfo, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1336:31: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1336 | nbv->setAtomProperties(gmx::constArrayRefFromArray(mdatoms->typeA, mdatoms->nr),
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1337 | gmx::constArrayRefFromArray(mdatoms->chargeA, mdatoms->nr), fr->cginfo);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1336:31: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1409:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1409 | nbv->convertCoordinates(AtomLocality::Local, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1409:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1487:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1487 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1505:51: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1505 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1513:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1513 | nbv->convertCoordinates(AtomLocality::NonLocal, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1513:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1674:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1674 | nbv->dispatchFreeEnergyKernel(InteractionLocality::Local, fr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1675 | as_rvec_array(x.unpaddedArrayRef().data()),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1676 | &forceOutNonbonded->forceWithShiftForces(), *mdatoms,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1677 | inputrec->fepvals, lambda, enerd, stepWork, nrnb);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1681:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1681 | nbv->dispatchFreeEnergyKernel(InteractionLocality::NonLocal, fr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1682 | as_rvec_array(x.unpaddedArrayRef().data()),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1683 | &forceOutNonbonded->forceWithShiftForces(), *mdatoms,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1684 | inputrec->fepvals, lambda, enerd, stepWork, nrnb);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1713:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1713 | nbnxn_atomdata_add_nbat_fshift_to_fshift(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
1714 | *nbv->nbat, forceOutNonbonded->forceWithShiftForces().shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1732:35: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1732 | real dvdl_walls = do_walls(*inputrec, *fr, box, *mdatoms, x.unpaddedConstArrayRef(),
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | &forceOutMtsLevel0.forceWithVirial(), lambda[efptVDW],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | enerd->grpp.ener[egLJSR].data(), nrnb);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1764:35: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1764 | listedForces.calculate(
| ~~~~~~~~~~~~~~~~~~~~~~^
1765 | wcycle, box, inputrec->fepvals, cr, ms, x, xWholeMolecules, fr->fcdata.get(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1766 | hist, &forceOut, fr, &pbc, enerd, nrnb, lambda.data(), mdatoms,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1767 | DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1773:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1773 | calculateLongRangeNonbondeds(fr, inputrec, cr, nrnb, wcycle, mdatoms,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1774 | x.unpaddedConstArrayRef(), &forceOutMtsLevel1->forceWithVirial(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1775 | enerd, box, lambda.data(), as_rvec_array(dipoleData.muStateAB),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1776 | stepWork, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:645:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
645 | enerd->foreignLambdaTerms.finalizePotentialContributions(enerd->dvdl_lin, lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
646 | *inputrec->fepvals);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:645:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:645:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:651:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
651 | enerd->term[F_COM_PULL] += awh->applyBiasForcesAndUpdateBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
652 | inputrec->pbcType, mdatoms->massT, foreignLambdaDeltaH, foreignLambdaDhDl, box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
653 | forceWithVirial, t, step, wcycle, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:651:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:651:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1845:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1845 | stateGpu->copyForcesToGpu(forceOutMtsLevel0.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1846 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1855:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1855 | stateGpu->copyForcesFromGpu(forceOutMtsLevel0.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1856 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1866:57: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1866 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat, forceWithShiftForces.shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1901:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1901 | stateGpu->copyForcesToGpu(forceOutMtsLevel0.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1902 | AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2032:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2032 | stateGpu->copyForcesToGpu(forceWithShift, locality);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2049:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2049 | stateGpu->copyForcesFromGpu(forceWithShift, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2072:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2072 | postProcessForceWithShiftForces(nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutMtsLevel0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2073 | vir_force, *mdatoms, *fr, vsite, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2072:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2077:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2077 | postProcessForceWithShiftForces(nrnb, wcycle, box, x.unpaddedArrayRef(), forceOutMtsLevel1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2078 | vir_force, *mdatoms, *fr, vsite, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2077:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2100:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2100 | postProcessForces(cr, step, nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutCombined,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2101 | vir_force, mdatoms, fr, vsite, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2105:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2105 | postProcessForces(cr, step, nrnb, wcycle, box, x.unpaddedArrayRef(), forceOutMtsLevel1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2106 | vir_force, mdatoms, fr, vsite, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2116:36: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2116 | accumulatePotentialEnergies(enerd, lambda, inputrec->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2100:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2100 | postProcessForces(cr, step, nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutCombined,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2101 | vir_force, mdatoms, fr, vsite, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2072:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2072 | postProcessForceWithShiftForces(nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutMtsLevel0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2073 | vir_force, *mdatoms, *fr, vsite, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2072:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp: In function 'void do_md_trajectory_writing(FILE*, t_commrec*, int, const t_filenm*, int64_t, int64_t, double, t_inputrec*, t_state*, t_state*, ObservablesHistory*, const gmx_mtop_t*, t_forcerec*, gmx_mdoutf_t, const gmx::EnergyOutput&, gmx_ekindata_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:58:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
58 | void do_md_trajectory_writing(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:149:41: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
149 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step, t, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
150 | state_global, observablesHistory, f, &checkpointDataHolder);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_gpu_impl.cpp: In member function 'void gmx::UpdateConstrainGpu::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_gpu_impl.cpp:73:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
73 | void UpdateConstrainGpu::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In member function 'void gmx::Update::Impl::update_sd_second_half(const t_inputrec&, int64_t, real*, const t_mdatoms*, t_state*, const t_commrec*, t_nrnb*, gmx_wallcycle_t, gmx::Constraints*, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1403:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1403 | constr->apply(do_log, do_ene, step, 1, 0.5, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1404 | xp_.arrayRefWithPadding(), ArrayRef<RVec>(), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1405 | state->lambda[efptBONDED], dvdlambda, state->v.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1406 | computeVirial, nullptr, ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp: In function 'gmx::RangePartitioning gmx::makeUpdateGroups(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp:340:26: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
340 | static RangePartitioning makeUpdateGroups(const gmx_moltype_t& moltype, gmx::ArrayRef<const t_iparams> iparams)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp:359:85: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
359 | FlexibleConstraintTreatment::Include);
| ^
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp: In member function 'void gmx::UpdateGroupsCog::addCogs(gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:80:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
80 | void UpdateGroupsCog::addCogs(gmx::ArrayRef<const int> globalAtomIndices,
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp: In function 'void calc_vcm_grp(const t_mdatoms&, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const gmx::BasicVector<double> >, t_vcm*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp:155:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
155 | void calc_vcm_grp(const t_mdatoms& md,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp:155:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp: In function 'void process_and_stopcm_grp(FILE*, t_vcm*, const t_mdatoms&, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp:579:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
579 | void process_and_stopcm_grp(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp:579:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::Update::setNumAtoms(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::Update::Impl::Impl(const t_inputrec&, gmx::BoxDeformation*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wholemoleculetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/wholemoleculetransform.cpp: In member function 'void gmx::WholeMoleculeTransform::updateForAtomPbcJumps(gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/wholemoleculetransform.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
57 | void WholeMoleculeTransform::updateForAtomPbcJumps(ArrayRef<const RVec> x, const matrix box)
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/wholemoleculetransform.cpp: In member function 'gmx::ArrayRef<const gmx::BasicVector<double> > gmx::WholeMoleculeTransform::wholeMoleculeCoordinates(gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/wholemoleculetransform.cpp:62:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
62 | ArrayRef<const RVec> WholeMoleculeTransform::wholeMoleculeCoordinates(ArrayRef<const RVec> x, const matrix box)
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp: In function 'real do_walls(const t_inputrec&, const t_forcerec&, const real (*)[3], const t_mdatoms&, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ForceWithVirial*, real, real*, t_nrnb*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp:162:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
162 | real do_walls(const t_inputrec& ir,
| ^~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void gmx::construct_vsites_thread(gmx::ArrayRef<gmx::BasicVector<double> >, real, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<const t_iparams>, gmx::ArrayRef<const InteractionList>, const t_pbc*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:625:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
625 | static void construct_vsites_thread(ArrayRef<RVec> x,
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:625:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:625:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void gmx::construct_vsites(const gmx::ThreadingInfo*, gmx::ArrayRef<gmx::BasicVector<double> >, real, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<const t_iparams>, gmx::ArrayRef<const InteractionList>, const gmx::DomainInfo&, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:769:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
769 | static void construct_vsites(const ThreadingInfo* threadingInfo,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:769:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:769:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:809:32: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
809 | construct_vsites_thread(x, dt, v, ip, ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:835:32: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
835 | construct_vsites_thread(x, dt, v, ip, threadingInfo->threadDataNonLocalDependent().ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function '_ZN3gmxL16construct_vsitesEPKNS_13ThreadingInfoENS_8ArrayRefINS_11BasicVectorIdEEEEdS6_NS3_IK9t_iparamsEENS3_IK15InteractionListEERKNS_10DomainInfoEPA3_Kd._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:822:40: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
822 | construct_vsites_thread(x, dt, v, ip, tData.ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:829:44: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
829 | construct_vsites_thread(x, dt, v, ip, tData.idTask.ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void gmx::spreadForceForThread(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], gmx::ArrayRef<const t_iparams>, gmx::ArrayRef<const InteractionList>, const t_pbc*) [with gmx::VirtualSitesHandler::VirialHandling virialHandling = gmx::VirtualSitesHandler::VirialHandling::NonLinear]':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1728:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1728 | static void spreadForceForThread(ArrayRef<const RVec> x,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1728:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1728:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1728:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void gmx::spreadForceWrapper(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::VirialHandling, gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], bool, gmx::ArrayRef<const t_iparams>, gmx::ArrayRef<const InteractionList>, const t_pbc*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1823:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1823 | static void spreadForceWrapper(ArrayRef<const RVec> x,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1823:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1823:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1823:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1847:60: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1847 | spreadForceForThread<VirialHandling::NonLinear>(x, f, fshift, dxdf, ip, ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1847:60: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:396:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
396 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:396:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:418:45: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
418 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, neighborLambdaDhdl,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
419 | forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:418:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationgrid.h:105:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
105 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:105:29: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
105 | gmx::ArrayRef<const double> Bias::calcForceAndUpdateBias(const awh_dvec coordValue,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:105:29: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:105:29: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
146 | convolvedBias = state_.updateProbabilityWeightsAndConvolvedBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
147 | dimParams_, grid_, moveUmbrella ? neighborLambdaEnergies : ArrayRef<const double>{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | &probWeightNeighbor);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:152:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
152 | updateForceCorrelationGrid(probWeightNeighbor, neighborLambdaDhdl, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:152:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:152:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:154:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
154 | state_.sampleCoordAndPmf(dimParams_, grid_, probWeightNeighbor, convolvedBias);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:154:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
168 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
169 | moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
170 | tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
180 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
181 | dimParams_, grid_, coordState.umbrellaGridpoint(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
182 | moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{}, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
192 | state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, neighborLambdaDhdl,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
193 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
180 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
181 | dimParams_, grid_, coordState.umbrellaGridpoint(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
182 | moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{}, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
146 | convolvedBias = state_.updateProbabilityWeightsAndConvolvedBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
147 | dimParams_, grid_, moveUmbrella ? neighborLambdaEnergies : ArrayRef<const double>{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | &probWeightNeighbor);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function '_ZN3gmx19VirtualSitesHandler4Impl12spreadForcesENS_8ArrayRefIKNS_11BasicVectorIdEEEENS2_IS4_EENS0_14VirialHandlingES7_PA3_dP6t_nrnbPA3_KdP13gmx_wallcycle._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2006:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2006 | spreadForceWrapper(x, f, virialHandling, fshift_t, tData.dxdf, false, iparams_,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2007 | tData.ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2006:35: note: parameter passing for argument of type 'const gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1969:39: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1969 | spreadForceWrapper(x, idTask->force, virialHandling, fshift_t, tData.dxdf, true,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1970 | iparams_, tData.idTask.ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1969:39: note: parameter passing for argument of type 'const gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp: In member function 'real gmx::Awh::applyBiasForcesAndUpdateBias(PbcType, const real*, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, const real (*)[3], gmx::ForceWithVirial*, double, int64_t, gmx_wallcycle*, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:294:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
294 | real Awh::applyBiasForcesAndUpdateBias(PbcType pbcType,
| ^~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:294:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:352:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
352 | &biasPotentialJump, commRecord_, multiSimRecord_, t, step, seed_, fplog);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:352:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:352:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In member function 'void gmx::VirtualSitesHandler::Impl::construct(gmx::ArrayRef<gmx::BasicVector<double> >, real, gmx::ArrayRef<gmx::BasicVector<double> >, const real (*)[3]) const':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:839:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
839 | void VirtualSitesHandler::Impl::construct(ArrayRef<RVec> x, real dt, ArrayRef<RVec> v, const matrix box) const
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:839:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:841:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
841 | construct_vsites(&threadingInfo_, x, dt, v, iparams_, ilists_, domainInfo_, box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:841:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:841:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:841:21: note: parameter passing for argument of type 'const gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In member function 'void gmx::VirtualSitesHandler::construct(gmx::ArrayRef<gmx::BasicVector<double> >, real, gmx::ArrayRef<gmx::BasicVector<double> >, const real (*)[3]) const':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:844:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
844 | void VirtualSitesHandler::construct(ArrayRef<RVec> x, real dt, ArrayRef<RVec> v, const matrix box) const
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:844:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:846:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
846 | impl_->construct(x, dt, v, box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:846:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:846:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void gmx::constructVirtualSites(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<const t_iparams>, gmx::ArrayRef<const InteractionList>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:849:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
849 | void constructVirtualSites(ArrayRef<RVec> x, ArrayRef<const t_iparams> ip, ArrayRef<const InteractionList> ilist)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:849:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:854:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
854 | construct_vsites(nullptr, x, 0, {}, ip, ilist, domainInfo, nullptr);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:854:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:854:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:854:21: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void gmx::constructVirtualSitesGlobal(const gmx_mtop_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:917:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
917 | void constructVirtualSitesGlobal(const gmx_mtop_t& mtop, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In member function 'void gmx::VirtualSitesHandler::Impl::spreadForces(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::VirtualSitesHandler::VirialHandling, gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], t_nrnb*, const real (*)[3], gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1868:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1868 | void VirtualSitesHandler::Impl::spreadForces(ArrayRef<const RVec> x,
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1868:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1868:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1868:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1868:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1898:26: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1898 | dd_clear_f_vsites(*domainInfo_.domdec_, f);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1906:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1906 | spreadForceWrapper(x, f, virialHandling, fshift, dxdf, true, iparams_, ilists_, pbc_null);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1906:27: note: parameter passing for argument of type 'const gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1923:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1923 | spreadForceWrapper(x, f, virialHandling, fshift, nlDependentVSites.dxdf, true, iparams_,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1924 | nlDependentVSites.ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1923:27: note: parameter passing for argument of type 'const gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2043:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2043 | dd_move_f_vsites(*domainInfo_.domdec_, f, fshift);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2043:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2043:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In member function 'void gmx::VirtualSitesHandler::spreadForces(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::VirtualSitesHandler::VirialHandling, gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], t_nrnb*, const real (*)[3], gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2097:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2097 | void VirtualSitesHandler::spreadForces(ArrayRef<const RVec> x,
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2097:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2097:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2106:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2106 | impl_->spreadForces(x, f, virialHandling, fshift, virial, nrnb, box, wcycle);
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2106:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2106:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2106:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In member function 'void gmx::ThreadingInfo::setVirtualSites(gmx::ArrayRef<const InteractionList>, gmx::ArrayRef<const t_iparams>, const t_mdatoms&, bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2425:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
2425 | void ThreadingInfo::setVirtualSites(ArrayRef<const InteractionList> ilists,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In member function 'void gmx::VirtualSitesHandler::Impl::setVirtualSites(gmx::ArrayRef<const InteractionList>, const t_mdatoms&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2688:35: note: parameter passing for argument of type 'const gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
2688 | threadingInfo_.setVirtualSites(ilists, iparams_, mdatoms, domainInfo_.useDomdec());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2688:35: note: parameter passing for argument of type 'const gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.h:70,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:48:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*, int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/memory:63,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.cpp:47:
/usr/include/c++/10/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >; _Predicate = __gnu_cxx::__ops::_Iter_pred<gmx::BiasGrid::hasLambdaAxis() const::<lambda(const auto:22&)> >]':
/usr/include/c++/10/bits/stl_algobase.h:1921:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
1921 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~
/usr/include/c++/10/bits/stl_algobase.h:1921:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biassharing.cpp
/usr/include/c++/10/bits/stl_algobase.h: In function 'bool gmx::pointsAlongLambdaAxis(const gmx::BiasGrid&, int, int)':
/usr/include/c++/10/bits/stl_algobase.h:1974:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
1974 | return __find_if(__first, __last, __pred,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
1975 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algobase.h: In function 'bool gmx::pointsHaveDifferentLambda(const gmx::BiasGrid&, int, int)':
/usr/include/c++/10/bits/stl_algobase.h:1974:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
1974 | return __find_if(__first, __last, __pred,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
1975 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/dimparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.h:61,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, int, const int&, bool}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function '_ZN3gmx13ThreadingInfo15setVirtualSitesENS_8ArrayRefIK15InteractionListEENS1_IK9t_iparamsEERK9t_mdatomsb._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::BiasGrid::BiasGrid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, int, int&, bool}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&, bool}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::BiasGrid&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biaswriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/coordstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:351:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
351 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::BiasGrid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const BiasGrid& grid,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, int, gmx::ArrayRef<const double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:475:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
475 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:475:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
508 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:529:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
529 | calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, neighborLambdaDhdl, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:529:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
539 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:549:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
549 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
550 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:549:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:553:69: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
553 | double newPotential = calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
554 | dimParams, grid, coordState_.umbrellaGridpoint(), neighborLambdaDhdl, newForce);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:553:69: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::BiasGrid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1350:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1350 | void BiasState::sampleProbabilityWeights(const BiasGrid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1404:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1404 | void BiasState::sampleCoordAndPmf(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'double gmx::BiasState::updateProbabilityWeightsAndConvolvedBias(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >*) const':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1242:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1242 | double BiasState::updateProbabilityWeightsAndConvolvedBias(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/pointstate.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
78 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/read_params.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
210 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:243:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
243 | newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:243:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfitting.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1159 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1160 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual const std::vector<double>& gmx::{anonymous}::UnitAmplitudes::operator()(const t_mdatoms&, gmx::ArrayRef<const int>)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp: In member function 'void gmx::DensityFittingForceProvider::Impl::calculateForces(const gmx::ForceProviderInput&, gmx::ForceProviderOutput*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp:276:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
276 | (*affineTransformation_)(transformedCoordinates_);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp:292:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
292 | transformationToDensityLattice_(transformedCoordinates_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp:340:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
340 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(forces_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp
In file included from /usr/include/c++/10/bits/node_handle.h:39,
from /usr/include/c++/10/bits/hashtable.h:37,
from /usr/include/c++/10/unordered_map:46,
from /usr/include/c++/10/functional:61,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp:44:
/usr/include/c++/10/optional: In constructor 'gmx::DensityFittingForceProvider::Impl::Impl(const gmx::DensityFittingParameters&, gmx::basic_mdspan<const float, gmx::extents<-1, -1, -1> >, const gmx::TranslateAndScale&, const gmx::LocalAtomSet&, PbcType, double, const gmx::DensityFittingForceProviderState&)':
/usr/include/c++/10/optional:418:4: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >' changed in GCC 7.1
418 | ::new
| ^~~~~
419 | (std::__addressof(static_cast<_Dp*>(this)->_M_payload._M_payload))
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
420 | _Stored_type(std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp: In member function 'void ListedForces::calculate(gmx_wallcycle*, const real (*)[3], const t_lambda*, const t_commrec*, const gmx_multisim_t*, gmx::ArrayRefWithPadding<const gmx::BasicVector<double> >, gmx::ArrayRef<const gmx::BasicVector<double> >, t_fcdata*, history_t*, gmx::ForceOutputs*, const t_forcerec*, const t_pbc*, gmx_enerdata_t*, t_nrnb*, const real*, const t_mdatoms*, int*, const gmx::StepWorkload&)':
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp:698:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
698 | void ListedForces::calculate(struct gmx_wallcycle* wcycle,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp:760:55: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
760 | enerd->term[F_ORIRESDEV] = calc_orires_dev(
| ~~~~~~~~~~~~~~~^
761 | ms, idef.il[F_ORIRES].size(), idef.il[F_ORIRES].iatoms.data(), idef.iparams.data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
762 | md, xWholeMolecules, x, fr->bMolPBC ? pbc : nullptr, fcdata->orires, hist);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp: In function 'real calc_orires_dev(const gmx_multisim_t*, int, const t_iatom*, const t_iparams*, const t_mdatoms*, gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3], const t_pbc*, t_oriresdata*, history_t*)':
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp:384:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
384 | real calc_orires_dev(const gmx_multisim_t* ms,
| ^~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:555:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
555 | static void pme_load_balance(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_loadbal_do(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, t_forcerec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_wallcycle_t, int64_t, int64_t, gmx_bool*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:901:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
901 | void pme_loadbal_do(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:1040:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1040 | pme_load_balance(pme_lb, cr, fp_err, fp_log, mdlog, ir, box, x,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1041 | pme_lb->cycles_c - cycles_prev, fr->ic, fr->nbv.get(), &fr->pmedata, step);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'void gmx_pme_calc_energy(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const double>, real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:950:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
950 | void gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q, real* V)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:950:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:75:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:75:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'int gmx_pmeonly(gmx_pme_t*, const t_commrec*, t_nrnb*, gmx_wallcycle*, gmx_walltime_accounting_t, t_inputrec*, PmeRunMode, const gmx::DeviceStreamManager*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:720:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
720 | stateGpu->copyCoordinatesToGpu(gmx::ArrayRef<gmx::RVec>(pme_pp->x), gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:737:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
737 | gmx_pme_do(pme, pme_pp->x, pme_pp->f, pme_pp->chargeA.data(), pme_pp->chargeB.data(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
738 | pme_pp->sqrt_c6A.data(), pme_pp->sqrt_c6B.data(), pme_pp->sigmaA.data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
739 | pme_pp->sigmaB.data(), box, cr, maxshift_x, maxshift_y, mynrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
740 | output.coulombVirial_, output.lennardJonesVirial_, &output.coulombEnergy_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
741 | &output.lennardJonesEnergy_, lambda_q, lambda_lj, &dvdlambda_q,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
742 | &dvdlambda_lj, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:737:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:737:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void dd_pmeredist_f(gmx_pme_t*, PmeAtomComm*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:388:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
388 | void dd_pmeredist_f(struct gmx_pme_t* pme, PmeAtomComm* atc, gmx::ArrayRef<gmx::RVec> f, gmx_bool bAddF)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'int gmx_pme_do(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, real*, real*, real*, real*, real*, real*, const real (*)[3], const t_commrec*, int, int, t_nrnb*, gmx_wallcycle*, real (*)[3], real (*)[3], real*, real*, real, real, real*, real*, const gmx::StepWorkload&)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1002:5: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1002 | int gmx_pme_do(struct gmx_pme_t* pme,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1002:5: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1151:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1151 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, coefficient);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1151:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1368:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1368 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, RedistC6);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1368:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1377:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1377 | do_redist_pos_coeffs(pme, cr, FALSE, coordinates, RedistSigma);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1377:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void do_redist_pos_coeffs(gmx_pme_t*, const t_commrec*, gmx_bool, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:453:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
453 | void do_redist_pos_coeffs(struct gmx_pme_t* pme,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -MF CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/device_stream_manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/device_context.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/device_stream.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/device_management_common.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/prepare_detection.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/prepare_detection.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/prepare_detection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/prepare_detection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/device_management.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/md.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/membedholder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:51:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:51:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp: In member function 'void gmx::LegacySimulator::do_mimic()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:227:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
227 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:300:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
300 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
301 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, nullptr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
302 | force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
303 | &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:300:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:305:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
305 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
306 | makeConstArrayRef(state->x), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
307 | &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:392:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
392 | vsite->construct(state->x, ir->delta_t, state->v, state->box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:392:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:392:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:424:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
424 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
425 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
426 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
427 | state->v.arrayRefWithPadding(), state->box, state->lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
428 | &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
429 | fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:440:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
440 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
441 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
442 | &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
443 | vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:453:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
453 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
454 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
455 | energyOutput, ekind, f.view().force(), isCheckpointingStep,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
456 | doRerun, isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:468:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
468 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
469 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
470 | enerd, nullptr, nullptr, nullptr, nullptr, constr, &signaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
471 | state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
472 | CGLO_GSTAT | CGLO_ENERGY
| ~~~~~~~~~~~~~~~~~~~~~~~~
473 | | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
474 | : 0));
| ~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:468:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:475:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
475 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
476 | &top, makeConstArrayRef(state->x), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:487:31: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
487 | dd_collect_vec(cr->dd, state->ddp_count, state->ddp_count_cg_gl, state->cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
488 | flocal, ftemp);
| ~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:487:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:512:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
512 | accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:257:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
257 | initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:515:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
515 | vsite->construct(state->x, ir->delta_t, {}, state->box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:515:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:515:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:586:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
586 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
587 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
588 | enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
589 | state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
590 | cglo_flags_iteration
| ~~~~~~~~~~~~~~~~~~~~
591 | | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
592 | : 0));
| ~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:586:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:600:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
600 | process_and_stopcm_grp(fplog, &vcm, *mdatoms, x, makeArrayRef(state->v));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:600:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:600:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:604:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
604 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
605 | makeConstArrayRef(state->x), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
606 | &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:615:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
615 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
616 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
617 | enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
618 | state->box, nullptr, &bSumEkinhOld, cglo_flags & ~CGLO_PRESSURE);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:615:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:737:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
737 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:741:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
741 | pme_loadbal_do(pme_loadbal, cr, (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
742 | fplog, mdlog, *ir, fr, state->box, state->x, wcycle, step, step_rel,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
743 | &bPMETunePrinting, simulationWork.useGpuPmePpCommunication);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:798:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
798 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:803:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
803 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:865:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
865 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
866 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
867 | enerd, nullptr, nullptr, nullptr, nullptr, constr, &nullSignaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
868 | state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
869 | CGLO_GSTAT | CGLO_TEMPERATURE | CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:865:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:870:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
870 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
871 | &top, makeConstArrayRef(state->x), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
872 | &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:918:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
918 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
919 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
920 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
921 | state->v.arrayRefWithPadding(), state->box, state->lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
922 | &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
923 | fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:945:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
945 | do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
946 | nrnb, wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
947 | &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
948 | vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
949 | (bNS ? GMX_FORCE_NS : 0) | force_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1007:32: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1007 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1008 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1009 | enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1010 | state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1011 | (bGStat ? CGLO_GSTAT : 0) | (bCalcEner ? CGLO_ENERGY : 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1012 | | (bTemp ? CGLO_TEMPERATURE : 0) | (bPres ? CGLO_PRESSURE : 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1013 | | (bPres ? CGLO_CONSTRAINT : 0) | (bStopCM ? CGLO_STOPCM : 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1014 | | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1015 | : 0)
| ~~~~
1016 | | CGLO_SCALEEKIN);
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1007:32: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1024:48: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1024 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1025 | top_global, &top, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1026 | state->box, &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1029:43: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1029 | process_and_stopcm_grp(fplog, &vcm, *mdatoms, makeArrayRef(state->x),
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1030 | makeArrayRef(state->v));
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1029:43: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1029:43: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1068:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1068 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1069 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1070 | enerd, nullptr, nullptr, nullptr, nullptr, constr, &nullSignaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1071 | state->box, nullptr, &bSumEkinhOld, CGLO_GSTAT | CGLO_TEMPERATURE);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1068:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1099:50: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1099 | accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1127:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1127 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1135:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1135 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1151:40: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1151 | stateGpu->copyForcesFromGpu(f.view().force(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1158:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1158 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1159 | observablesHistory, top_global, fr, outf, energyOutput, ekind,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1160 | f.view().force(), checkpointHandler->isCheckpointingStep(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1161 | bRerunMD, bLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1193:55: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1193 | bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, &upd, constr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1268:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1268 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1269:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1269 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1276:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1276 | stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1282:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1282 | stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1289:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1289 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1290 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1291 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1292 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1299:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1299 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1345:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1345 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1346 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1347 | force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, lastbox,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1348 | nullptr, &bSumEkinhOld, (bGStat ? CGLO_GSTAT : 0) | CGLO_TEMPERATURE);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1345:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1391:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1391 | vsite->construct(state->x, ir->delta_t, state->v, state->box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1391:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1391:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1410:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1410 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1423:32: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1423 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1424 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1425 | wcycle, enerd, force_vir, shake_vir, total_vir, pres, constr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1426 | &signaller, lastbox, &totalNumberOfBondedInteractions, &bSumEkinhOld,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1427 | (bGStat ? CGLO_GSTAT : 0) | (!EI_VV(ir->eI) && bCalcEner ? CGLO_ENERGY : 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1428 | | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1429 | | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1430 | | (!EI_VV(ir->eI) ? CGLO_PRESSURE : 0) | CGLO_CONSTRAINT
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1431 | | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1432 | : 0));
| ~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1423:32: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1433:48: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1433 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1434 | top_global, &top, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1435 | state->box, &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1438:43: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1438 | process_and_stopcm_grp(fplog, &vcm, *mdatoms, makeArrayRef(state->x),
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1439 | makeArrayRef(state->v));
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1438:43: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1438:43: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1445:55: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1445 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1453:58: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1453 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1471:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1471 | accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1572:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1572 | printLambdaStateToLog(fplog, state->lambda, isInitialOutput);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void {anonymous}::EnergyEvaluator::run(em_state_t*, real*, real (*)[3], real (*)[3], int64_t, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:834:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
834 | vsite->construct(ems->s.x, 1, {}, ems->s.box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:834:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:834:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:848:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
848 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, count, nrnb, wcycle,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
849 | top, ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist, &ems->f.view(), force_vir,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
850 | mdAtoms->mdatoms(), enerd, ems->s.lambda, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
851 | GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES | GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
852 | | (bNS ? GMX_FORCE_NS : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
853 | DDBalanceRegionHandler(cr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:896:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
896 | constr->apply(needsLogging, computeEnergy, count, 0, 1.0, ems->s.x.arrayRefWithPadding(), f,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
897 | f.unpaddedArrayRef(), ems->s.box, ems->s.lambda[efptBONDED], &dvdl_constr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
898 | gmx::ArrayRefWithPadding<RVec>(), computeVirial, shake_vir,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
899 | gmx::ConstraintVariable::ForceDispl);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:913:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
913 | accumulateKineticLambdaComponents(enerd, ems->s.lambda, *inputrec->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void init_em(FILE*, const gmx::MDLogger&, const char*, const t_commrec*, t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, const gmx_mtop_t*, em_state_t*, gmx_localtop_t*, t_nrnb*, t_forcerec*, gmx::MDAtoms*, gmx_global_stat**, gmx::VirtualSitesHandler*, gmx::Constraints*, gmx_shellfc_t**)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:397:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
397 | initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:461:26: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
461 | constr->apply(needsLogging, computeEnergy, -1, 0, 1.0, ems->s.x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
462 | ems->s.x.arrayRefWithPadding(), ArrayRef<RVec>(), ems->s.box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
463 | ems->s.lambda[efptFEP], &dvdl_constr, gmx::ArrayRefWithPadding<RVec>(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
464 | computeVirial, nullptr, gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, const gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:539:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
539 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
540 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
541 | observablesHistory, state->f.view().force(), &checkpointDataHolder);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:551:31: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
551 | dd_collect_vec(cr->dd, state->s.ddp_count, state->s.ddp_count_cg_gl, state->s.cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
552 | state->s.x, globalXRef);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:551:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, const gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:539:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
539 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
540 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
541 | observablesHistory, state->f.view().force(), &checkpointDataHolder);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_lbfgs()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1765:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1765 | vsite->construct(state_global->x, 1, {}, state_global->box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1765:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1765:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1867:41: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1867 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1868 | static_cast<real>(step), &ems.s, state_global, observablesHistory,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1869 | ems.f.view().force(), &checkpointDataHolder);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_nm()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:2774:40: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
2774 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, nullptr, step, inputrec,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2775 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2776 | state_work.s.natoms, state_work.s.x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2777 | state_work.s.v.arrayRefWithPadding(), state_work.s.box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2778 | state_work.s.lambda, &state_work.s.hist, &state_work.f.view(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2779 | vir, mdatoms, nrnb, wcycle, shellfc, fr, runScheduleWork, t,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2780 | mu_tot, vsite, DDBalanceRegionHandler(nullptr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp: In member function 'void gmx::LegacySimulator::do_rerun()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:285:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
285 | initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:354:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
354 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
355 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, nullptr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
356 | force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
357 | &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:354:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:359:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
359 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
360 | makeConstArrayRef(state->x), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
361 | &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:165:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
165 | vsite->construct(globalState->x, timeStep, globalState->v, globalState->box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:165:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:165:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:540:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
540 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
541 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
542 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
543 | state->v.arrayRefWithPadding(), state->box, state->lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
544 | &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
545 | fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:556:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
556 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
557 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
558 | &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
559 | vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:569:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
569 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
570 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
571 | energyOutput, ekind, f.view().force(), isCheckpointingStep,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
572 | doRerun, isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:580:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
580 | vsite->construct(state->x, ir->delta_t, state->v, state->box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:580:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:580:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:591:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
591 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
592 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
593 | enerd, force_vir, shake_vir, total_vir, pres, constr, &signaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
594 | state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
595 | CGLO_GSTAT | CGLO_ENERGY
| ~~~~~~~~~~~~~~~~~~~~~~~~
596 | | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
597 | : 0));
| ~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:591:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:598:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
598 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
599 | &top, makeConstArrayRef(state->x), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
600 | &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'bool do_em_step(const t_commrec*, t_inputrec*, t_mdatoms*, em_state_t*, real, gmx::ArrayRefWithPadding<const gmx::BasicVector<double> >, em_state_t*, gmx::Constraints*, int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:689:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
689 | validStep = constr->apply(
| ~~~~~~~~~~~~~^
690 | TRUE, TRUE, count, 0, 1.0, s1->x.arrayRefWithPadding(), s2->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
691 | ArrayRef<RVec>(), s2->box, s2->lambda[efptBONDED], &dvdl_constr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
692 | gmx::ArrayRefWithPadding<RVec>(), false, nullptr, gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function 'void pr_shell(FILE*, gmx::ArrayRef<const t_shell>)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:126:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_shell>' changed in GCC 7.1
126 | static void pr_shell(FILE* fplog, ArrayRef<const t_shell> shells)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function 'real rms_force(const t_commrec*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const t_shell>, int, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:778:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_shell>' changed in GCC 7.1
778 | static real rms_force(const t_commrec* cr,
| ^~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_shell&}; _Tp = t_shell; _Alloc = std::allocator<t_shell>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_shell>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::make_local_shells(const t_commrec*, const t_mdatoms*, gmx_shellfc_t*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_shell*, std::vector<t_shell> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationinput.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationinputhandle.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function 'void init_adir(gmx_shellfc_t*, gmx::Constraints*, const t_inputrec*, const t_commrec*, int, int64_t, const t_mdatoms*, int, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, const real (*)[3], gmx::ArrayRef<const double>, real*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:828:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
828 | static void init_adir(gmx_shellfc_t* shfc,
| ^~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:890:18: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
890 | constr->apply(needsLogging, computeEnergy, step, 0, 1.0, xCurrent,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
891 | shfc->adir_xnold.arrayRefWithPadding(), {}, box, lambda[efptBONDED],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
892 | &(dvdlambda[efptBONDED]), {}, computeVirial, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
893 | gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:894:18: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
894 | constr->apply(needsLogging, computeEnergy, step, 0, 1.0, xCurrent,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
895 | shfc->adir_xnew.arrayRefWithPadding(), {}, box, lambda[efptBONDED],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
896 | &(dvdlambda[efptBONDED]), {}, computeVirial, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
897 | gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:910:18: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
910 | constr->apply(needsLogging, computeEnergy, step, 0, 1.0, xOld, shfc->adir_xnew.arrayRefWithPadding(),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
911 | acc_dir, box, lambda[efptBONDED], &(dvdlambda[efptBONDED]), {}, computeVirial,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
912 | nullptr, gmx::ConstraintVariable::Deriv_FlexCon);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function 'gmx_shellfc_t* init_shell_flexcon(FILE*, const gmx_mtop_t*, int, int, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:427:41: note: parameter passing for argument of type 'gmx::ArrayRef<const t_shell>' changed in GCC 7.1
427 | pr_shell(fplog, shell);
| ~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:498:17: note: parameter passing for argument of type 'gmx::ArrayRef<const t_shell>' changed in GCC 7.1
498 | pr_shell(debug, shell);
| ~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulatorbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function 'void relax_shell_flexcon(FILE*, const t_commrec*, const gmx_multisim_t*, gmx_bool, gmx_enfrot*, int64_t, const t_inputrec*, gmx::ImdSession*, pull_t*, gmx_bool, int, const gmx_localtop_t*, gmx::Constraints*, gmx_enerdata_t*, int, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, const real (*)[3], gmx::ArrayRef<double>, history_t*, gmx::ForceBuffersView*, real (*)[3], const t_mdatoms*, t_nrnb*, gmx_wallcycle_t, gmx_shellfc_t*, t_forcerec*, gmx::MdrunScheduleWorkload*, double, real*, gmx::VirtualSitesHandler*, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:915:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
915 | void relax_shell_flexcon(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1039:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1039 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, mdstep,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1040 | nrnb, wcycle, top, box, xPadded, hist, &forceViewInit, force_vir, md, enerd, lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1041 | fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1042 | (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1055:32: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1055 | accumulatePotentialEnergies(enerd, lambda, inputrec->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1047:18: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1047 | init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end, shfc->x_old.arrayRefWithPadding(),
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1048 | x, xPadded, force[Min], shfc->acc_dir, box, lambda, &dum);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1104:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1104 | vsite->construct(pos[Min], inputrec->delta_t, v, box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1104:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1104:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1109:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1109 | init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1110 | shfc->x_old.arrayRefWithPadding(), x, posWithPadding[Min], force[Min],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1111 | shfc->acc_dir, box, lambda, &dum);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1126:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1126 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, 1, nrnb, wcycle,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1127 | top, box, posWithPadding[Try], hist, &forceViewTry, force_vir, md, enerd, lambda, fr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1128 | runScheduleWork, vsite, mu_tot, t, nullptr, shellfc_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1129:36: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1129 | accumulatePotentialEnergies(enerd, lambda, inputrec->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1138:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1138 | init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1139 | shfc->x_old.arrayRefWithPadding(), x, posWithPadding[Try], force[Try],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1140 | shfc->acc_dir, box, lambda, &dum);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp: In member function 'void gmx::LegacySimulator::do_tpi()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:605:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
605 | nbnxn_put_on_grid(fr->nbv.get(), box, 0, vzero, boxDiagonal, nullptr, { 0, a_tp0 }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
606 | fr->cginfo, x, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:677:34: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
677 | nbnxn_put_on_grid(fr->nbv.get(), box, 1, x_init, x_init, nullptr, { a_tp0, a_tp1 },
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
678 | -1, fr->cginfo, x, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:681:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
681 | fr->nbv->setAtomProperties(gmx::constArrayRefFromArray(mdatoms->typeA, mdatoms->nr),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
682 | gmx::constArrayRefFromArray(mdatoms->chargeA, mdatoms->nr),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
683 | fr->cginfo);
| ~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:681:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:738:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
738 | fr->nbv->convertCoordinates(AtomLocality::NonLocal, false, x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:738:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:756:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
756 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
757 | wcycle, &top, state_global->box, state_global->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
758 | &state_global->hist, &f.view(), force_vir, mdatoms, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
759 | state_global->lambda, fr, runScheduleWork, nullptr, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
760 | GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY | (bStateChanged ? GMX_FORCE_STATECHANGED : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
761 | DDBalanceRegionHandler(nullptr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/10/bits/unique_ptr.h: In member function 'int gmx::Mdrunner::mdrunner()':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:1245:51: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1245 | putUpdateGroupAtomsInSamePeriodicImage(*cr->dd, mtop, globalState->box, globalState->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:1245:51: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:1526:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1526 | constructVirtualSitesGlobal(mtop, globalState->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -MF CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o.d -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyCoordinatesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:129:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
129 | void StatePropagatorDataGpu::copyCoordinatesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_x */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyCoordinatesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:144:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
144 | void StatePropagatorDataGpu::copyCoordinatesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_x */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyVelocitiesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:161:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
161 | void StatePropagatorDataGpu::copyVelocitiesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_v */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyVelocitiesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:177:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
177 | void StatePropagatorDataGpu::copyVelocitiesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_v */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyForcesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:201:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
201 | void StatePropagatorDataGpu::copyForcesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_f */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyForcesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
226 | void StatePropagatorDataGpu::copyForcesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_f */,
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -MF CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o.d -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -MF CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -MF CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o.d -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -MF CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o.d -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -MF CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/options.cpp.o -MF CMakeFiles/libgromacs.dir/options/options.cpp.o.d -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -MF CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o.d -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -MF CMakeFiles/libgromacs.dir/options/optionsection.cpp.o.d -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -MF CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o.d -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -MF CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -MF CMakeFiles/libgromacs.dir/options/treesupport.cpp.o.d -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/manager.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintpotential.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const int&}; _Tp = gmx::Site; _Alloc = std::allocator<gmx::Site>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::Site>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr<gmx::IRestraintPotential>, const std::vector<int>&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::Site*, std::vector<gmx::Site> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/confio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp: In static member function 'static void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:271:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
271 | void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::RVec> forces, int natoms)
| ^~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/espio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/groio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/matio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/md5.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 'void writeXpmAxis(FILE*, const char*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:830:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
830 | static void writeXpmAxis(FILE* out, const char* axis, ArrayRef<const real> label)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:116:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
116 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx_tng_add_mtop(gmx_tng_trajectory_t, const gmx_mtop_t*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -MF CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<t_matrix> read_xpm_matrix(const char*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -MF CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionbehavior.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::internal::{anonymous}::computeMassesAndCharges(const gmx_mtop_t*, const gmx_ana_pos_t&, std::vector<double>*, std::vector<double>*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::internal::SelectionData::initializeMassesAndCharges(const gmx_mtop_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selelem.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selelem.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selhelp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selmethod.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selvalue.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_compare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_insolidangle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_keywords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_merge.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_permute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_position.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_same.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_simple.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/symrec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_d.so.6 -o ../../lib/libgromacs_d.so.6.0.0 CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o CMakeFiles/libgromacs.dir/utility/any.cpp.o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o CMakeFiles/libgromacs.dir/utility/compare.cpp.o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o CMakeFiles/libgromacs.dir/utility/futil.cpp.o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o CMakeFiles/libgromacs.dir/utility/init.cpp.o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o CMakeFiles/libgromacs.dir/utility/logger.cpp.o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o CMakeFiles/libgromacs.dir/utility/path.cpp.o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o CMakeFiles/libgromacs.dir/domdec/box.cpp.o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o CMakeFiles/libgromacs.dir/math/functions.cpp.o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o CMakeFiles/libgromacs.dir/math/matrix.cpp.o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o CMakeFiles/libgromacs.dir/math/optimization.cpp.o CMakeFiles/libgromacs.dir/math/units.cpp.o CMakeFiles/libgromacs.dir/math/utilities.cpp.o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o CMakeFiles/libgromacs.dir/random/seed.cpp.o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o CMakeFiles/libgromacs.dir/topology/block.cpp.o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o CMakeFiles/libgromacs.dir/topology/idef.cpp.o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o CMakeFiles/libgromacs.dir/topology/index.cpp.o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o CMakeFiles/libgromacs.dir/topology/topology.cpp.o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o CMakeFiles/libgromacs.dir/pulling/output.cpp.o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o CMakeFiles/libgromacs.dir/simd/support.cpp.o CMakeFiles/libgromacs.dir/imd/imd.cpp.o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o CMakeFiles/libgromacs.dir/tools/check.cpp.o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o CMakeFiles/libgromacs.dir/tools/dump.cpp.o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl.cpp.o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o CMakeFiles/libgromacs.dir/fft/fft.cpp.o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o CMakeFiles/libgromacs.dir/hardware/prepare_detection.cpp.o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o CMakeFiles/libgromacs.dir/options/options.cpp.o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o CMakeFiles/libgromacs.dir/selection/params.cpp.o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o CMakeFiles/libgromacs.dir/selection/position.cpp.o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o CMakeFiles/libgromacs.dir/selection/selection.cpp.o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/nrjac.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o selection/CMakeFiles/scanner.dir/parser.cpp.o selection/CMakeFiles/scanner.dir/scanner.cpp.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so -lpthread -lm /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.6.0.0 ../../lib/libgromacs_d.so.6 ../../lib/libgromacs_d.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target libgromacs
/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend
/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/box.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/forcecalculator.cpp.o -MF CMakeFiles/nblib.dir/forcecalculator.cpp.o.d -o CMakeFiles/nblib.dir/forcecalculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.6.0.0 /usr/lib/arm-linux-gnueabihf/libX11.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target gmx
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxsetup.cpp.o -MF CMakeFiles/nblib.dir/gmxsetup.cpp.o.d -o CMakeFiles/nblib.dir/gmxsetup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/integrator.cpp
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp: In member function 'void nblib::ForceCalculator::updatePairList(gmx::ArrayRef<const int>, gmx::ArrayRef<gmx::BasicVector<double> >, const nblib::Box&)':
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:73:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
73 | void ForceCalculator::updatePairList(gmx::ArrayRef<const int> particleInfoAllVdW,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:77:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
77 | gmxForceCalculator_->setParticlesOnGrid(particleInfoAllVdW, coordinates, box);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:77:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp: In member function 'void nblib::ForceCalculator::compute(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:63:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
63 | void ForceCalculator::compute(gmx::ArrayRef<const Vec3> coordinates, gmx::ArrayRef<Vec3> forces)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:63:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:70:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
70 | gmxForceCalculator_->compute(coordinates, forces);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:70:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:70:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/interactions.cpp
/<<PKGBUILDDIR>>/api/nblib/integrator.cpp: In member function 'void nblib::LeapFrog::integrate(real, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/api/nblib/integrator.cpp:63:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
63 | void LeapFrog::integrate(const real dt, gmx::ArrayRef<Vec3> x, gmx::ArrayRef<Vec3> v, gmx::ArrayRef<const Vec3> f)
| ^~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/integrator.cpp:63:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/integrator.cpp:63:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/molecules.cpp
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp: In member function 'void nblib::GmxForceCalculator::compute(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
70 | void GmxForceCalculator::compute(gmx::ArrayRef<const gmx::RVec> coordinateInput,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:74:29: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
74 | nbv_->convertCoordinates(gmx::AtomLocality::Local, false, coordinateInput);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:74:29: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp: In member function 'void nblib::GmxForceCalculator::setParticlesOnGrid(gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, const nblib::Box&)':
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:82:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
82 | void GmxForceCalculator::setParticlesOnGrid(gmx::ArrayRef<const int> particleInfoAllVdw,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:82:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:97:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
97 | nbnxn_put_on_grid(nbv_.get(), legacyBox, 0, lowerCorner, upperCorner, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
98 | { 0, int(coordinates.size()) }, particleDensity, particleInfoAllVdw,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
99 | coordinates, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/particlesequencer.cpp
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp: In member function 'void nblib::NbvSetupUtil::setAtomProperties(const std::vector<int>&, const std::vector<double>&)':
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp:172:49: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
172 | gmxForceCalculator_->nbv_->setAtomProperties(particleTypeIdOfAllParticles, charges, particleInfoAllVdw_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp:172:49: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp: In member function 'void nblib::NbvSetupUtil::setParticlesOnGrid(const std::vector<gmx::BasicVector<double> >&, const nblib::Box&)':
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp:298:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
298 | gmxForceCalculator_->setParticlesOnGrid(particleInfoAllVdw_, coordinates, box);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp:298:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp: In member function 'void nblib::NbvSetupUtil::setupNbnxmInstance(size_t, const nblib::NBKernelOptions&)':
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp:199:24: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
199 | nbnxn_atomdata_init(gmx::MDLogger(), atomData.get(), kernelSetup.kernelType, combinationRule,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | numParticleTypes, nonbondedParameters_, 1, numThreads);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/api/nblib/vector.h:47,
from /<<PKGBUILDDIR>>/api/nblib/gmxcalculator.h:52,
from /<<PKGBUILDDIR>>/api/nblib/gmxsetup.h:51,
from /<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void nblib::NbvSetupUtil::setNonBondedParameters(const std::vector<nblib::ParticleType>&, const nblib::NonBondedInteractionMap&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/particletype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/simulationstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/topologyhelpers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/topology.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nblib::ParticleData}; _Tp = nblib::ParticleData; _Alloc = std::allocator<nblib::ParticleData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::ParticleData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >, {nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>}>::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&}; unsigned int ...__indices = {0}]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::HarmonicAngleType&}; _Tp = nblib::HarmonicAngleType; _Alloc = std::allocator<nblib::HarmonicAngleType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::ProperDihedral&}; _Tp = nblib::ProperDihedral; _Alloc = std::allocator<nblib::ProperDihedral>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::Default5Center&}; _Tp = nblib::Default5Center; _Alloc = std::allocator<nblib::Default5Center>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >, {nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>}>::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&}; unsigned int ...__indices = {1}]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::CubicBondType&}; _Tp = nblib::CubicBondType; _Alloc = std::allocator<nblib::CubicBondType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >, {nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>}>::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&}; unsigned int ...__indices = {2}]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::CubicBondType*, std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >, {nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>}>::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&}; unsigned int ...__indices = {3}]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >, {nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>}>::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&}; unsigned int ...__indices = {4}]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::ImproperDihedral&}; _Tp = nblib::ImproperDihedral; _Alloc = std::allocator<nblib::ImproperDihedral>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::RyckaertBellemanDihedral&}; _Tp = nblib::RyckaertBellemanDihedral; _Alloc = std::allocator<nblib::RyckaertBellemanDihedral>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void nblib::Molecule::addInteraction(const nblib::ParticleIdentifier&, const nblib::ParticleIdentifier&, const nblib::ParticleIdentifier&, const nblib::ParticleIdentifier&, const nblib::ParticleIdentifier&, const FiveCenterInteraction&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::Default5Center*, std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>, {nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>}>::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>&}; unsigned int ...__indices = {1}]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::ImproperDihedral*, std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>, {nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>}>::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>&}; unsigned int ...__indices = {2}]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::RyckaertBellemanDihedral*, std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>, {nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>}>::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>&}; unsigned int ...__indices = {0}]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::ProperDihedral*, std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void nblib::Molecule::addInteraction(const nblib::ParticleIdentifier&, const nblib::ParticleIdentifier&, const nblib::ParticleIdentifier&, const ThreeCenterInteraction&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::HarmonicAngleType*, std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/transformations.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'nblib::Molecule& nblib::Molecule::addParticle(const ParticleName&, const ResidueName&, const Charge&, const nblib::ParticleType&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::ParticleData*, std::vector<nblib::ParticleData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp: In member function 'void nblib::ListedForceCalculator::computeForcesAndEnergies(gmx::ArrayRef<const gmx::BasicVector<double> >, bool)':
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:85:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
85 | void ListedForceCalculator::computeForcesAndEnergies(gmx::ArrayRef<const Vec3> x, bool usePbc)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp: In member function 'void nblib::ListedForceCalculator::compute(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, bool)':
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:137:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
137 | void ListedForceCalculator::compute(gmx::ArrayRef<const Vec3> coordinates, gmx::ArrayRef<Vec3> forces, bool usePbc)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:137:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:151:29: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
151 | computeForcesAndEnergies(coordinates, usePbc);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp: In member function 'void nblib::ListedForceCalculator::compute(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, nblib::ListedForceCalculator::EnergyType&, bool)':
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:159:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
159 | void ListedForceCalculator::compute(gmx::ArrayRef<const Vec3> coordinates,
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:159:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:164:12: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
164 | compute(coordinates, forces, usePbc);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:164:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:164:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/util/setup.cpp
/<<PKGBUILDDIR>>/api/nblib/util/setup.cpp: In function 'bool nblib::isRealValued(gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/api/nblib/util/setup.cpp:124:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
124 | bool isRealValued(gmx::ArrayRef<const Vec3> values)
| ^~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::RyckaertBellemanDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/util/setup.cpp: In function 'void nblib::zeroCartesianArray(gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/api/nblib/util/setup.cpp:139:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
139 | void zeroCartesianArray(gmx::ArrayRef<Vec3> cartesianArray)
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::RyckaertBellemanDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::RyckaertBellemanDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function '_ForwardIterator std::__upper_bound(_ForwardIterator, _ForwardIterator, const _Tp&, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >; _Tp = std::tuple<nblib::ProperDihedral, unsigned int>; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ProperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:2053:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
2053 | __upper_bound(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:2053:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ProperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ProperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::ProperDihedral, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ProperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::HarmonicAngleType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ImproperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::CubicBondType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::Default5Center>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::CubicBondType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ImproperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::HarmonicAngleType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::Default5Center>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::CubicBondType, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::CubicBondType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::HarmonicAngleType, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::HarmonicAngleType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::ImproperDihedral, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ImproperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::Default5Center, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::Default5Center>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::ParticleType&}; _Tp = nblib::ParticleType; _Alloc = std::allocator<nblib::ParticleType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::ParticleType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::CubicBondType&}; _Tp = nblib::CubicBondType; _Alloc = std::allocator<nblib::CubicBondType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::CubicBondType]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::CubicBondType*, std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::HarmonicAngleType&}; _Tp = nblib::HarmonicAngleType; _Alloc = std::allocator<nblib::HarmonicAngleType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::ProperDihedral&}; _Tp = nblib::ProperDihedral; _Alloc = std::allocator<nblib::ProperDihedral>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::ImproperDihedral&}; _Tp = nblib::ImproperDihedral; _Alloc = std::allocator<nblib::ImproperDihedral>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::RyckaertBellemanDihedral&}; _Tp = nblib::RyckaertBellemanDihedral; _Alloc = std::allocator<nblib::RyckaertBellemanDihedral>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::Default5Center&}; _Tp = nblib::Default5Center; _Alloc = std::allocator<nblib::Default5Center>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::Default5Center]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::Default5Center*, std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::RyckaertBellemanDihedral]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::RyckaertBellemanDihedral*, std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::ImproperDihedral]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::ImproperDihedral*, std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::HarmonicAngleType]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::HarmonicAngleType*, std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::ProperDihedral]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::ProperDihedral*, std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::CubicBondType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::CubicBondType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::CubicBondType]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::CubicBondType*, std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::HarmonicAngleType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::HarmonicAngleType>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::HarmonicAngleType]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::HarmonicAngleType*, std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ProperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ProperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::ProperDihedral]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:2169:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
2169 | = std::__upper_bound(++__middle, __first, __val, __comp_val_it);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::ProperDihedral*, std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h:2133:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >' changed in GCC 7.1
2133 | return std::__upper_bound(__first, __last, __val,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2134 | __gnu_cxx::__ops::__val_comp_iter(__comp));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ImproperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ImproperDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::ImproperDihedral]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::ImproperDihedral*, std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::RyckaertBellemanDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::RyckaertBellemanDihedral>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::RyckaertBellemanDihedral]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::RyckaertBellemanDihedral*, std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::Default5Center>::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::Default5Center]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::Default5Center*, std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'nblib::Topology nblib::TopologyBuilder::buildTopology()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::ParticleType*, std::vector<nblib::ParticleType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib.so.0 -o ../../lib/libnblib.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/forcecalculator.cpp.o CMakeFiles/nblib.dir/gmxcalculator.cpp.o CMakeFiles/nblib.dir/gmxsetup.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o ../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib.so.0.1.0 ../../lib/libnblib.so.0 ../../lib/libnblib.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target nblib
/usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend
/usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/samples /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/samples /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build
/usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:57,
from /<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:57,
from /<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp: In function 'int main()':
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:89:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
89 | };
| ^
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:96:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
96 | };
| ^
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:103:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
103 | };
| ^
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:120:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
120 | forceCalculator.compute(simState.coordinates(), userForces);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:120:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:120:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:129:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
129 | integrator.integrate(1.0, simState.coordinates(), simState.velocities(), simState.forces());
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:129:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:129:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:129:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -o ../../../bin/argon-forces-integration ../../../lib/libnblib.so.0.1.0 -Wl,-rpath-link,/<<PKGBUILDDIR>>/build/basic-dp/lib
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp: In function 'int main()':
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:157:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
157 | };
| ^
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:172:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
172 | };
| ^
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:201:32: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
201 | forceCalculator.compute(simulationState.coordinates(), simulationState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:201:32: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:201:32: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:203:38: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
203 | listedForceCalculator.compute(simulationState.coordinates(), simulationState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:203:38: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:203:38: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:206:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
206 | integrator.integrate(1.0, simulationState.coordinates(), simulationState.velocities(),
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
207 | simulationState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:206:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:206:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:206:29: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target argon-forces-integration
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -o ../../../bin/methane-water-integration ../../../lib/libnblib.so.0.1.0 -Wl,-rpath-link,/<<PKGBUILDDIR>>/build/basic-dp/lib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target methane-water-integration
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -j4 -C build/basic tests
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/make -f CMakeFiles/Makefile2 tests
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles 95
/usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
/usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/depend
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googletest /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3.9 -D HAVE_FULL_FUNCTIONING_PYTHON=Python3_Interpreter_FOUND -D PROJECT_VERSION=2021.3-Raspbian-2021.3-4 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2021.3-4 -D SOURCE_IS_SOURCE_DISTRIBUTION=ON -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoWithoutGit.cmake
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -Dgtest_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googletest/include -I/<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -Wshadow -Werror -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=c++17 -MD -MT src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-all.cc
Consolidate compiler generated dependencies of target mdrun_objlib
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 0%] Built target release-version-info
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
Consolidate compiler generated dependencies of target scanner
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build
[ 0%] Built target mdrun_objlib
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
[ 0%] Built target scanner
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
Consolidate compiler generated dependencies of target lmfit_objlib
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
Consolidate compiler generated dependencies of target tng_io_obj
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
[ 0%] Built target lmfit_objlib
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
[ 2%] Built target tng_io_obj
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
Consolidate compiler generated dependencies of target thread_mpi
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
Consolidate compiler generated dependencies of target linearalgebra
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 4%] Built target thread_mpi
[ 4%] Built target linearalgebra
Consolidate compiler generated dependencies of target modularsimulator
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 5%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Consolidate compiler generated dependencies of target libgromacs
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 64%] Built target libgromacs
/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib /<<PKGBUILDDIR>>/build/basic/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake --color=
Consolidate compiler generated dependencies of target nblib
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 65%] Built target nblib
/usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend
/usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/samples /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib/samples /<<PKGBUILDDIR>>/build/basic/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/samples /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib/samples /<<PKGBUILDDIR>>/build/basic/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake --color=
Consolidate compiler generated dependencies of target methane-water-integration
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
Consolidate compiler generated dependencies of target argon-forces-integration
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 65%] Built target methane-water-integration
[ 66%] Built target argon-forces-integration
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so -o ../../../../../lib/libgtest.so CMakeFiles/gtest.dir/src/gtest-all.cc.o -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 66%] Built target gtest
/usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -Wshadow -Werror -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++17 -MD -MT src/external/googletest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o -MF CMakeFiles/gmock.dir/src/gmock-all.cc.o.d -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googlemock/src/gmock-all.cc
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so -o ../../../../lib/libgmock.so CMakeFiles/gmock.dir/src/gmock-all.cc.o ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 66%] Built target gmock
/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/testutils /<<PKGBUILDDIR>>/build/basic/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/cmdlinetest.cpp.o -MF CMakeFiles/testutils.dir/cmdlinetest.cpp.o.d -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/cmdlinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/conftest.cpp.o -MF CMakeFiles/testutils.dir/conftest.cpp.o.d -o CMakeFiles/testutils.dir/conftest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/conftest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/filematchers.cpp.o -MF CMakeFiles/testutils.dir/filematchers.cpp.o.d -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/filematchers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/interactivetest.cpp.o -MF CMakeFiles/testutils.dir/interactivetest.cpp.o.d -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/interactivetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/loggertest.cpp.o -MF CMakeFiles/testutils.dir/loggertest.cpp.o.d -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/loggertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/mpi_printer.cpp.o -MF CMakeFiles/testutils.dir/mpi_printer.cpp.o.d -o CMakeFiles/testutils.dir/mpi_printer.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpi_printer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/mpitest.cpp.o -MF CMakeFiles/testutils.dir/mpitest.cpp.o.d -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/refdata.cpp.o -MF CMakeFiles/testutils.dir/refdata.cpp.o.d -o CMakeFiles/testutils.dir/refdata.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/refdata_xml.cpp.o -MF CMakeFiles/testutils.dir/refdata_xml.cpp.o.d -o CMakeFiles/testutils.dir/refdata_xml.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata_xml.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/simulationdatabase.cpp.o -MF CMakeFiles/testutils.dir/simulationdatabase.cpp.o.d -o CMakeFiles/testutils.dir/simulationdatabase.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/simulationdatabase.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/stdiohelper.cpp.o -MF CMakeFiles/testutils.dir/stdiohelper.cpp.o.d -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stdiohelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/stringtest.cpp.o -MF CMakeFiles/testutils.dir/stringtest.cpp.o.d -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stringtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/testasserts.cpp.o -MF CMakeFiles/testutils.dir/testasserts.cpp.o.d -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testasserts.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/testfilemanager.cpp.o -MF CMakeFiles/testutils.dir/testfilemanager.cpp.o.d -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfilemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/testfileredirector.cpp.o -MF CMakeFiles/testutils.dir/testfileredirector.cpp.o.d -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/test_device.cpp.o -MF CMakeFiles/testutils.dir/test_device.cpp.o.d -o CMakeFiles/testutils.dir/test_device.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/test_device.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/test_hardware_environment.cpp.o -MF CMakeFiles/testutils.dir/test_hardware_environment.cpp.o.d -o CMakeFiles/testutils.dir/test_hardware_environment.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/test_hardware_environment.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/testinit.cpp.o -MF CMakeFiles/testutils.dir/testinit.cpp.o.d -o CMakeFiles/testutils.dir/testinit.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testinit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/testmatchers.cpp.o -MF CMakeFiles/testutils.dir/testmatchers.cpp.o.d -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testmatchers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/testoptions.cpp.o -MF CMakeFiles/testutils.dir/testoptions.cpp.o.d -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/textblockmatchers.cpp.o -MF CMakeFiles/testutils.dir/textblockmatchers.cpp.o.d -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/textblockmatchers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -MF CMakeFiles/testutils.dir/tprfilegenerator.cpp.o.d -o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tprfilegenerator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/xvgtest.cpp.o -MF CMakeFiles/testutils.dir/xvgtest.cpp.o.d -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/xvgtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -MF CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o.d -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /<<PKGBUILDDIR>>/src/external/tinyxml2/tinyxml2.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1
/usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi_printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata_xml.cpp.o CMakeFiles/testutils.dir/simulationdatabase.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/test_device.cpp.o CMakeFiles/testutils.dir/test_hardware_environment.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o
/usr/bin/ranlib ../../lib/libtestutils.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 68%] Built target testutils
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/depend
/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/depend
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/testutils/tests /<<PKGBUILDDIR>>/build/basic/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/testutils/tests /<<PKGBUILDDIR>>/build/basic/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib/tests /<<PKGBUILDDIR>>/build/basic/api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energyreader.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/mpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/interactivetest.cpp.o -MF CMakeFiles/testutils-test.dir/interactivetest.cpp.o.d -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/interactivetest.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/testhelpers.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/testhelpers.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/testhelpers.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/testhelpers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/testsystems.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -MF CMakeFiles/testutils-test.dir/refdata_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.6.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 68%] Built target testutils-mpi-test
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -MF CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 68%] Built target utility-mpi-test
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/alignedallocator.cpp.o -MF CMakeFiles/utility-test.dir/alignedallocator.cpp.o.d -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testhelpers.cpp.o CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o
/usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 69%] Built target nblib_test_infrastructure
/usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -MF CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o.d -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulatorcomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/terminationhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -MF CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/arrayref.cpp.o -MF CMakeFiles/utility-test.dir/arrayref.cpp.o.d -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.6.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 69%] Built target testutils-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectoryreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp
/usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp
/usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target mdrun_test_infrastructure
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask64.cpp.o -MF CMakeFiles/utility-test.dir/bitmask64.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energydrifttracker.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:235:80: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
235 | nullptr, step, step, seed_, nullptr);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:235:80: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:235:80: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energyoutput.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp: In member function 'virtual void gmx::test::BiasTest_DetectsCovering_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:320:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
320 | nullptr, step, step, params.awhParams.seed, nullptr);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:320:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:320:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasgrid.cpp.o -MF CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasgrid.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/dimparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.h:61,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasgrid.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::test::biasGridTest_neighborhood_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/expanded.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasstate.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/freeenergyparameters.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:41:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::BiasFepLambdaStateTest::BiasFepLambdaStateTest()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp: In member function 'virtual void gmx::test::BiasFepLambdaStateTest_ForcesBiasPmf_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:229:74: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | nullptr, nullptr, step * mdTimeStep, step, seed_, nullptr);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:229:74: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:229:74: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:41:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:41:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::test::BiasFepLambdaStateTest_DetectsCovering_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:309:67: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
309 | params.awhParams.seed, nullptr);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:309:67: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:309:67: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasgrid.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.6.0.0 ../../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target awh-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.6.0.0 ../../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target density_fitting_applied_forces-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/defaultinitializationallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -MF CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o.d -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/enumerationhelpers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp
/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/fixedcapacityvector.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_grp_tcstat&}; _Tp = t_grp_tcstat; _Alloc = std::allocator<t_grp_tcstat>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_grp_tcstat>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::LeapFrogTestData::LeapFrogTestData(int, real, const real*, const real*, int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::test::{anonymous}::iListInput; _Alloc = std::allocator<gmx::test::{anonymous}::iListInput>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:63,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:56:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<typename testing::internal::IteratorTraits<Iterator>::value_type> testing::ValuesIn(ForwardIterator, ForwardIterator) [with ForwardIterator = __gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >]':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:304:1: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
304 | ValuesIn(ForwardIterator begin, ForwardIterator end) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:304:1: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/inmemoryserializer.cpp
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_AngleZeroListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_RestraintsListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_BondZeroLengthListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_AngleListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_BondListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_PolarizeListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_DihedralListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:646:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
646 | std::vector<iListInput> c_InputBonds = {
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:661:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
661 | std::vector<iListInput> c_InputAngles = {
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:685:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
685 | std::vector<iListInput> c_InputDihs = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:695:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
695 | std::vector<iListInput> c_InputPols = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:705:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
705 | std::vector<iListInput> c_InputRestraints = {
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:715:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
715 | std::vector<iListInput> c_InputBondsZeroLength = {
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:720:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
720 | std::vector<iListInput> c_InputAnglesZeroAngle = {
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target applied_forces-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/listed_forces-test.dir/bonded.cpp.o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target listed_forces-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o
/usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target onlinehelp-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/haloexchange_mpi.cpp
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF CMakeFiles/domdec-test.dir/hashedmap.cpp.o.d -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/listoflists.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target domdec-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 71%] Built target domdec-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o -MF CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o.d -o CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mdmodulenotification-impl.cpp
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o -MF CMakeFiles/fft-test.dir/fft.cpp.o.d -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/mutex.cpp.o -MF CMakeFiles/utility-test.dir/mutex.cpp.o.d -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 71%] Built target fft-test
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/path.cpp.o -MF CMakeFiles/utility-test.dir/path.cpp.o.d -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/device_availability.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -MF CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o.d -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/device_stream_manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/range.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/expanded.cpp.o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 73%] Built target mdlib-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -MF CMakeFiles/hardware-test.dir/cpuinfo.cpp.o.d -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringutil.cpp.o -MF CMakeFiles/utility-test.dir/stringutil.cpp.o.d -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/device_management.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/cpuinfo.cpp.o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/hardware-test.dir/device_management.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 73%] Built target hardware-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -MF CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o.d -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -MF CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o.d -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/template_mp.cpp.o -MF CMakeFiles/utility-test.dir/template_mp.cpp.o.d -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/template_mp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -MF CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/pinnedmemorychecker.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 74%] Built target ewald-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -MF CMakeFiles/math-test.dir/coordinatetransformation.cpp.o.d -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/device_buffer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -MF CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/typecasts.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 74%] Built target gpu_utils-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfit.cpp.o -MF CMakeFiles/math-test.dir/densityfit.cpp.o.d -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfit.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -MF CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o.d -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/accessor_policy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textwriter.cpp.o -MF CMakeFiles/utility-test.dir/textwriter.cpp.o.d -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 75%] Built target mdrunutility-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/typetraits.cpp.o -MF CMakeFiles/utility-test.dir/typetraits.cpp.o.d -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/dofit.cpp.o -MF CMakeFiles/math-test.dir/dofit.cpp.o.d -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extents.cpp.o -MF CMakeFiles/mdspan-test.dir/extents.cpp.o.d -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extents.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -MF CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o.d -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/exponentialmovingaverage.cpp
/usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdtypes/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/tests/checkpointdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/listoflists.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/range.cpp.o CMakeFiles/utility-test.dir/strconvert.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/template_mp.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 77%] Built target utility-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extensions.cpp.o -MF CMakeFiles/mdspan-test.dir/extensions.cpp.o.d -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extensions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/tests/forcebuffers.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/layouts.cpp.o -MF CMakeFiles/mdspan-test.dir/layouts.cpp.o.d -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/layouts.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/gausstransform.cpp.o -MF CMakeFiles/math-test.dir/gausstransform.cpp.o.d -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/mdspan.cpp.o -MF CMakeFiles/mdspan-test.dir/mdspan.cpp.o.d -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/mdspan.cpp
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 77%] Built target mdtypes-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/multidimarray.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -MF CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o.d -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 78%] Built target onlinehelp-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/neldermead.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/optimization.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 78%] Built target mdspan-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -MF CMakeFiles/random-test.dir/exponentialdistribution.cpp.o.d -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = const double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'std::enable_if_t<is_same_v<typename std::remove_const<_Tp>::type, typename std::remove_const<U>::type>, void> gmx::test::compareViewsIgnoreConst(gmx::ArrayRef<T>, gmx::ArrayRef<U>) [with T = double; U = const double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
100 | compareViewsIgnoreConst(ArrayRef<T> input, ArrayRef<U> output)
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:111:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
111 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:111:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/com.cpp.o CMakeFiles/pbcutil-test.dir/mshift.cpp.o CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target pbcutil-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/vectypes.cpp.o -MF CMakeFiles/math-test.dir/vectypes.cpp.o.d -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'std::enable_if_t<is_same_v<typename std::remove_const<_Tp>::type, typename std::remove_const<U>::type>, void> gmx::test::compareViewsIgnoreConst(gmx::ArrayRef<T>, gmx::ArrayRef<U>) [with T = gmx::BasicVector<double>; U = const gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
100 | compareViewsIgnoreConst(ArrayRef<T> input, ArrayRef<U> output)
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = const gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF CMakeFiles/options-test.dir/repeatingsection.cpp.o.d -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_InternalCounterSequence_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Using40Rounds_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Default_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/neldermead.cpp.o CMakeFiles/math-test.dir/optimization.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Fast_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:117:54: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
117 | const std::vector<uint64_t> bitsZero{ { 0, 0, 0, 0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:127:87: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
127 | 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:136:86: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
136 | 0xa4093822299f31d0ULL, 0x082efa98ec4e6c89ULL } };
| ^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target math-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:46:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:46:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 82%] Built target taskassignment-test
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 82%] Built target table-test
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 82%] Built target random-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 82%] Built target options-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/mtop.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 82%] Built target pull-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/mp11.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/idef.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 83%] Built target topology-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/mp11.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 83%] Built target compat-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target gmxana-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 85%] Built target pdb2gmx3-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_integer.cpp.o -MF CMakeFiles/simd-test.dir/simd_integer.cpp.o.d -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 85%] Built target pdb2gmx2-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 85%] Built target pdb2gmx1-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genion.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genrestr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/autocorr.cpp.o -MF CMakeFiles/correlations-test.dir/autocorr.cpp.o.d -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 86%] Built target simd-test
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/builder.cpp.o -MF CMakeFiles/coordinateio-test.dir/builder.cpp.o.d -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/builder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -MF CMakeFiles/correlations-test.dir/correlationdataset.cpp.o.d -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/correlationdataset.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/expfit.cpp.o -MF CMakeFiles/correlations-test.dir/expfit.cpp.o.d -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/mock_datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -MF CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o.d -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadapters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 87%] Built target correlations-test
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target gmxpreprocess-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target energyanalysis-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o
/usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target analysisdata-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/helpwriting.cpp
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/checkpoint.cpp.o -MF CMakeFiles/fileio-test.dir/checkpoint.cpp.o.d -o CMakeFiles/fileio-test.dir/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report_methods.cpp
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -MF CMakeFiles/coordinateio-test.dir/setatoms.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/trjconv.cpp.o -MF CMakeFiles/tool-test.dir/trjconv.cpp.o.d -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setbothtime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/helpwriting.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target tool-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -MF CMakeFiles/coordinateio-test.dir/settimestep.cpp.o.d -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/poscalc.cpp.o -MF CMakeFiles/selection-test.dir/poscalc.cpp.o.d -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/testmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/densityfittingmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 89%] Built target coordinateio-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/domain_decomposition.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/readinp.cpp.o -MF CMakeFiles/fileio-test.dir/readinp.cpp.o.d -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 90%] Built target mdrun-modules-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -MF CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/fileioxdrserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/tngio.cpp.o -MF CMakeFiles/fileio-test.dir/tngio.cpp.o.d -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xvgio.cpp.o -MF CMakeFiles/fileio-test.dir/xvgio.cpp.o.d -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pme-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 90%] Built target mdrun-pme-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In static member function 'static void gmx::test::XvgioTest::compareValues(gmx::basic_mdspan<const double, gmx::extents<-1, -1> >, gmx::basic_mdspan<const double, gmx::extents<-1, -1> >)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:75:17: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
75 | static void compareValues(basic_mdspan<const double, dynamicExtents2D> ref,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:75:17: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In member function 'virtual void gmx::test::XvgioTest_readXvgIgnoreCommentLineWorks_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:150:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
150 | compareValues(xvgRefData.asConstView(), xvgTestData.asConstView());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:150:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In member function 'virtual void gmx::test::XvgioTest_readXvgRealWorks_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:132:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
132 | compareValues(xvgRefData.asConstView(), xvgTestData.asConstView());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:132:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In member function 'virtual void gmx::test::XvgioTest_readXvgIntWorks_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:113:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
113 | compareValues(xvgRefData.asConstView(), xvgTestData.asConstView());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:113:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/checkpoint.cpp.o CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/xvgio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 91%] Built target fileio-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/checkpoint.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/ewaldsurfaceterm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -MF CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o.d -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multiple_time_stepping.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 92%] Built target selection-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/exactcontinuation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/orires.cpp.o -MF CMakeFiles/mdrun-test.dir/orires.cpp.o.d -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/periodicactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target mdrun-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target mdrun-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target mdrun-mpi-coordination-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target mdrun-simulator-comparison-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-io-test.dir/termination.cpp.o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target mdrun-io-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/outputfiles.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target mdrun-tpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/normalmodes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target mdrun-mpi-pme-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/freeenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -MF CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib/tests /<<PKGBUILDDIR>>/build/basic/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/box.cpp.o -MF CMakeFiles/nblib-setup-test.dir/box.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/box.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simple_mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -MF CMakeFiles/nblib-setup-test.dir/interactions.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target mdrun-output-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunfep-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrunfep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target mdrunfep-test
/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib/tests /<<PKGBUILDDIR>>/build/basic/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/particletype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target mdrun-non-integrator-test
/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib/tests /<<PKGBUILDDIR>>/build/basic/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp
/usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/bondtypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/pbcholder.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/helpers.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so ../../../lib/libgtest.so -lpthread ../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target nblib-integrator-test
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/nbnxnsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/molecules.cpp
/usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/util/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests /<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/util/tests/setup.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/simstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/util/tests/traits.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/kernels.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so ../../../lib/libgtest.so -lpthread ../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target nblib-integration-test
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-util-test.dir/setup.cpp.o CMakeFiles/nblib-util-test.dir/traits.cpp.o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target nblib-util-test
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/conversions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-setup-test.dir/box.cpp.o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o CMakeFiles/nblib-setup-test.dir/topology.cpp.o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so ../../../lib/libgtest.so -lpthread ../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target nblib-setup-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/transformations.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target mdrunutility-mpi-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 97%] Built target nblib-listed-forces-test
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 97%] Built target mdrunutility-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
/usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib /<<PKGBUILDDIR>>/build/basic/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 97%] Built target nblib-tests
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/average.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/filenm.cpp.o -MF CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF CMakeFiles/analysisdata-test.dir/histogram.cpp.o.d -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/pargs.cpp.o -MF CMakeFiles/commandline-test.dir/pargs.cpp.o.d -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/rdf.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 97%] Built target analysisdata-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target commandline-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target trajectoryanalysis-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/tests.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
(cd build/basic; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic/lib ctest -V || dpkg-architecture -i hurd-i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: NbLibListedForcesTests
1: Test command: /<<PKGBUILDDIR>>/build/basic/bin/nblib-listed-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/NbLibListedForcesTests.xml"
1: Test timeout computed to be: 600
1: [==========] Running 23 tests from 9 test cases.
1: [----------] Global test environment set-up.
1: [----------] 5 tests from NBlibTest
1: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks
1: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms)
1: [ RUN ] NBlibTest.BondTypesLessThanWorks
1: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms)
1: [ RUN ] NBlibTest.CanSplitListedWork
1: [ OK ] NBlibTest.CanSplitListedWork (1 ms)
1: [ RUN ] NBlibTest.ListedForceBuffer
1: [ OK ] NBlibTest.ListedForceBuffer (1 ms)
1: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct
1: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms)
1: [----------] 5 tests from NBlibTest (5 ms total)
1:
1: [----------] 1 test from Kernels
1: [ RUN ] Kernels.HarmonicScalarKernelCanCompute
1: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms)
1: [----------] 1 test from Kernels (1 ms total)
1:
1: [----------] 5 tests from ListedExampleData
1: [ RUN ] ListedExampleData.ComputeHarmonicBondForces
1: [ OK ] ListedExampleData.ComputeHarmonicBondForces (19 ms)
1: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies
1: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms)
1: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces
1: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (2 ms)
1: [ RUN ] ListedExampleData.CanReduceForces
1: [ OK ] ListedExampleData.CanReduceForces (1 ms)
1: [ RUN ] ListedExampleData.CanReduceEnergies
1: [ OK ] ListedExampleData.CanReduceEnergies (1 ms)
1: [----------] 5 tests from ListedExampleData (27 ms total)
1:
1: [----------] 1 test from LinearChainDataFixture
1: [ RUN ] LinearChainDataFixture.Multithreading
1: [ OK ] LinearChainDataFixture.Multithreading (1 ms)
1: [----------] 1 test from LinearChainDataFixture (3 ms total)
1:
1: [----------] 1 test from ListedShims
1: [ RUN ] ListedShims.ParameterConversion
1: [ OK ] ListedShims.ParameterConversion (0 ms)
1: [----------] 1 test from ListedShims (1 ms total)
1:
1: [----------] 1 test from ListedTransformations
1: [ RUN ] ListedTransformations.SortInteractionIndices
1: [ OK ] ListedTransformations.SortInteractionIndices (0 ms)
1: [----------] 1 test from ListedTransformations (1 ms total)
1:
1: [----------] 3 tests from FourCenter/ProperDihedralTest
1: [ RUN ] FourCenter/ProperDihedralTest.CheckListed/0
1: [ OK ] FourCenter/ProperDihedralTest.CheckListed/0 (1 ms)
1: [ RUN ] FourCenter/ProperDihedralTest.CheckListed/1
1: [ OK ] FourCenter/ProperDihedralTest.CheckListed/1 (1 ms)
1: [ RUN ] FourCenter/ProperDihedralTest.CheckListed/2
1: [ OK ] FourCenter/ProperDihedralTest.CheckListed/2 (1 ms)
1: [----------] 3 tests from FourCenter/ProperDihedralTest (5 ms total)
1:
1: [----------] 3 tests from TwoCenter/HarmonicBondTest
1: [ RUN ] TwoCenter/HarmonicBondTest.CheckListed/0
1: [ OK ] TwoCenter/HarmonicBondTest.CheckListed/0 (1 ms)
1: [ RUN ] TwoCenter/HarmonicBondTest.CheckListed/1
1: [ OK ] TwoCenter/HarmonicBondTest.CheckListed/1 (0 ms)
1: [ RUN ] TwoCenter/HarmonicBondTest.CheckListed/2
1: [ OK ] TwoCenter/HarmonicBondTest.CheckListed/2 (1 ms)
1: [----------] 3 tests from TwoCenter/HarmonicBondTest (5 ms total)
1:
1: [----------] 3 tests from ThreeCenter/HarmonicAngleTest
1: [ RUN ] ThreeCenter/HarmonicAngleTest.CheckListed/0
1: [ OK ] ThreeCenter/HarmonicAngleTest.CheckListed/0 (1 ms)
1: [ RUN ] ThreeCenter/HarmonicAngleTest.CheckListed/1
1: [ OK ] ThreeCenter/HarmonicAngleTest.CheckListed/1 (1 ms)
1: [ RUN ] ThreeCenter/HarmonicAngleTest.CheckListed/2
1: [ OK ] ThreeCenter/HarmonicAngleTest.CheckListed/2 (2 ms)
1: [----------] 3 tests from ThreeCenter/HarmonicAngleTest (7 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 23 tests from 9 test cases ran. (69 ms total)
1: [ PASSED ] 23 tests.
1/65 Test #1: NbLibListedForcesTests ................ Passed 2.95 sec
test 2
Start 2: NbLibSamplesTestArgon
2: Test command: /<<PKGBUILDDIR>>/build/basic/bin/argon-forces-integration
2: Test timeout computed to be: 1500
2: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000
2: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191
2: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000
2: final position of particle 0: x 0.789162 y 1.271508 z 0.819867
2/65 Test #2: NbLibSamplesTestArgon ................. Passed 0.18 sec
test 3
Start 3: NbLibSamplesTestMethaneWater
3: Test command: /<<PKGBUILDDIR>>/build/basic/bin/methane-water-integration
3: Test timeout computed to be: 1500
3: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000
3: final position of particle 9: x 0.132611 y 4.369854 z 5.148869
3/65 Test #3: NbLibSamplesTestMethaneWater .......... Passed 0.20 sec
test 4
Start 4: NbLibUtilTests
4: Test command: /<<PKGBUILDDIR>>/build/basic/bin/nblib-util-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/NbLibUtilTests.xml"
4: Test timeout computed to be: 30
4: [==========] Running 16 tests from 2 test cases.
4: [----------] Global test environment set-up.
4: [----------] 6 tests from NBlibTest
4: [ RUN ] NBlibTest.isRealValued
4: [ OK ] NBlibTest.isRealValued (0 ms)
4: [ RUN ] NBlibTest.checkNumericValuesHasNan
4: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms)
4: [ RUN ] NBlibTest.checkNumericValuesHasInf
4: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms)
4: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect
4: Velocities were taken from a Maxwell distribution at 300 K
4: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (2 ms)
4: [ RUN ] NBlibTest.generateVelocitySize
4: Velocities were taken from a Maxwell distribution at 300 K
4: [ OK ] NBlibTest.generateVelocitySize (0 ms)
4: [ RUN ] NBlibTest.generateVelocityCheckNumbers
4: Velocities were taken from a Maxwell distribution at 300 K
4: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms)
4: [----------] 6 tests from NBlibTest (2 ms total)
4:
4: [----------] 10 tests from NblibTraitsUtils
4: [ RUN ] NblibTraitsUtils.FuseTwo
4: [ OK ] NblibTraitsUtils.FuseTwo (0 ms)
4: [ RUN ] NblibTraitsUtils.Fuse
4: [ OK ] NblibTraitsUtils.Fuse (0 ms)
4: [ RUN ] NblibTraitsUtils.Repeat
4: [ OK ] NblibTraitsUtils.Repeat (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTuple1
4: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTuple2
4: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTypeList1
4: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTypeList2
4: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms)
4: [ RUN ] NblibTraitsUtils.Contains
4: [ OK ] NblibTraitsUtils.Contains (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated
4: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated
4: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms)
4: [----------] 10 tests from NblibTraitsUtils (0 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 16 tests from 2 test cases ran. (2 ms total)
4: [ PASSED ] 16 tests.
4/65 Test #4: NbLibUtilTests ........................ Passed 0.08 sec
test 5
Start 5: NbLibSetupTests
5: Test command: /<<PKGBUILDDIR>>/build/basic/bin/nblib-setup-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/NbLibSetupTests.xml"
5: Test timeout computed to be: 600
5: [==========] Running 39 tests from 1 test case.
5: [----------] Global test environment set-up.
5: [----------] 39 tests from NBlibTest
5: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN
5: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (1 ms)
5: [ RUN ] NBlibTest.CubicBoxCannotHaveInf
5: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms)
5: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN
5: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms)
5: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf
5: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms)
5: [ RUN ] NBlibTest.CubicBoxWorks
5: [ OK ] NBlibTest.CubicBoxWorks (0 ms)
5: [ RUN ] NBlibTest.NonBondedForceParamsCorrect
5: [ OK ] NBlibTest.NonBondedForceParamsCorrect (1 ms)
5: [ RUN ] NBlibTest.CanMergeInteractions
5: [ OK ] NBlibTest.CanMergeInteractions (0 ms)
5: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed
5: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms)
5: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed
5: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms)
5: [ RUN ] NBlibTest.PbcHolderWorks
5: [ OK ] NBlibTest.PbcHolderWorks (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms)
5: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule
5: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms)
5: [ RUN ] NBlibTest.CanConstructExclusionListFromNames
5: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms)
5: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed
5: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms)
5: [ RUN ] NBlibTest.AtWorks
5: [ OK ] NBlibTest.AtWorks (0 ms)
5: [ RUN ] NBlibTest.AtThrows
5: [ OK ] NBlibTest.AtThrows (0 ms)
5: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass
5: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (1 ms)
5: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass
5: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms)
5: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName
5: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms)
5: [ RUN ] NBlibTest.CanAddInteractions
5: [ OK ] NBlibTest.CanAddInteractions (0 ms)
5: [ RUN ] NBlibTest.TopologyHasNumParticles
5: [ OK ] NBlibTest.TopologyHasNumParticles (1 ms)
5: [ RUN ] NBlibTest.TopologyHasCharges
5: [ OK ] NBlibTest.TopologyHasCharges (0 ms)
5: [ RUN ] NBlibTest.TopologyHasMasses
5: [ OK ] NBlibTest.TopologyHasMasses (1 ms)
5: [ RUN ] NBlibTest.TopologyHasParticleTypes
5: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms)
5: [ RUN ] NBlibTest.TopologyHasParticleTypeIds
5: [ OK ] NBlibTest.TopologyHasParticleTypeIds (1 ms)
5: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType
5: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms)
5: [ RUN ] NBlibTest.TopologyHasExclusions
5: [ OK ] NBlibTest.TopologyHasExclusions (1 ms)
5: [ RUN ] NBlibTest.TopologyHasSequencing
5: [ OK ] NBlibTest.TopologyHasSequencing (0 ms)
5: [ RUN ] NBlibTest.TopologyCanAggregateBonds
5: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms)
5: [ RUN ] NBlibTest.TopologyCanSequencePairIDs
5: [ OK ] NBlibTest.TopologyCanSequencePairIDs (1 ms)
5: [ RUN ] NBlibTest.TopologySequenceIdThrows
5: No particle O-Atom in residue SOL in molecule SOL found
5: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms)
5: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds
5: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms)
5: [ RUN ] NBlibTest.TopologyListedInteractions
5: [ OK ] NBlibTest.TopologyListedInteractions (1 ms)
5: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes
5: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (1 ms)
5: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows
5: No particle Iron in residue SOL in molecule SOL found
5: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (1 ms)
5: [ RUN ] NBlibTest.toGmxExclusionBlockWorks
5: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms)
5: [----------] 39 tests from NBlibTest (12 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 39 tests from 1 test case ran. (12 ms total)
5: [ PASSED ] 39 tests.
5/65 Test #5: NbLibSetupTests ....................... Passed 0.09 sec
test 6
Start 6: NbLibIntegrationTests
6: Test command: /<<PKGBUILDDIR>>/build/basic/bin/nblib-integration-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/NbLibIntegrationTests.xml"
6: Test timeout computed to be: 600
6: [==========] Running 19 tests from 1 test case.
6: [----------] Global test environment set-up.
6: [----------] 19 tests from NBlibTest
6: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute
6: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (4 ms)
6: [ RUN ] NBlibTest.CanSetupStepWorkload
6: [ OK ] NBlibTest.CanSetupStepWorkload (0 ms)
6: [ RUN ] NBlibTest.GmxForceCalculatorCanSetupInteractionConst
6: [ OK ] NBlibTest.GmxForceCalculatorCanSetupInteractionConst (2 ms)
6: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect
6: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (2 ms)
6: [ RUN ] NBlibTest.ExpectedNumberOfForces
6: [ OK ] NBlibTest.ExpectedNumberOfForces (4 ms)
6: [ RUN ] NBlibTest.CanIntegrateSystem
6: [ OK ] NBlibTest.CanIntegrateSystem (3 ms)
6: [ RUN ] NBlibTest.UpdateChangesForces
6: [ OK ] NBlibTest.UpdateChangesForces (3 ms)
6: [ RUN ] NBlibTest.ArgonForcesAreCorrect
6: [ OK ] NBlibTest.ArgonForcesAreCorrect (2 ms)
6: [ RUN ] NBlibTest.CanConstructNbvSetupUtil
6: [ OK ] NBlibTest.CanConstructNbvSetupUtil (0 ms)
6: [ RUN ] NBlibTest.CanConstructSimulationState
6: [ OK ] NBlibTest.CanConstructSimulationState (1 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN
6: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (1 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF
6: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN
6: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (1 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF
6: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms)
6: [ RUN ] NBlibTest.SimulationStateCanMove
6: [ OK ] NBlibTest.SimulationStateCanMove (1 ms)
6: [ RUN ] NBlibTest.SimulationStateCanAssign
6: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms)
6: [ RUN ] NBlibTest.SimulationStateHasBox
6: [ OK ] NBlibTest.SimulationStateHasBox (1 ms)
6: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates
6: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms)
6: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities
6: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (1 ms)
6: [----------] 19 tests from NBlibTest (26 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 19 tests from 1 test case ran. (27 ms total)
6: [ PASSED ] 19 tests.
6/65 Test #6: NbLibIntegrationTests ................. Passed 0.10 sec
test 7
Start 7: NbLibIntegratorTests
7: Test command: /<<PKGBUILDDIR>>/build/basic/bin/nblib-integrator-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/NbLibIntegratorTests.xml"
7: Test timeout computed to be: 600
7: [==========] Running 1 test from 1 test case.
7: [----------] Global test environment set-up.
7: [----------] 1 test from NBlibTest
7: [ RUN ] NBlibTest.IntegratorWorks
7: [ OK ] NBlibTest.IntegratorWorks (1 ms)
7: [----------] 1 test from NBlibTest (2 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 1 test from 1 test case ran. (2 ms total)
7: [ PASSED ] 1 test.
7/65 Test #7: NbLibIntegratorTests .................. Passed 0.07 sec
test 8
Start 8: TestUtilsUnitTests
8: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsUnitTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 59 tests from 5 test cases.
8: [----------] Global test environment set-up.
8: [----------] 10 tests from InteractiveTestHelperTest
8: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
8: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (3 ms)
8: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
8: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (2 ms)
8: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
8: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
8: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
8: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
8: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
8: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
8: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
8: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
8: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (2 ms)
8: [----------] 10 tests from InteractiveTestHelperTest (20 ms total)
8:
8: [----------] 34 tests from ReferenceDataTest
8: [ RUN ] ReferenceDataTest.HandlesSimpleData
8: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
8: [ OK ] ReferenceDataTest.HandlesFloatingPointData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
8: [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesStringBlockData
8: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesVectorData
8: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesSequenceData
8: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
8: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesIncorrectData
8: [ OK ] ReferenceDataTest.HandlesIncorrectData (2 ms)
8: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
8: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMissingData
8: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUncheckedData
8: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
8: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
8: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesAnys
8: [ OK ] ReferenceDataTest.HandlesAnys (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
8: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
8: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
8: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue
8: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (2 ms)
8: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType
8: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (2 ms)
8: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
8: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
8: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
8: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
8: [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
8: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
8: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (2 ms)
8: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
8: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
8: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
8: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (2 ms)
8: [ RUN ] ReferenceDataTest.HandlesReadingValues
8: [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (2 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (2 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms)
8: [----------] 34 tests from ReferenceDataTest (41 ms total)
8:
8: [----------] 7 tests from FloatingPointDifferenceTest
8: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
8: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
8: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
8: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
8: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
8: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
8: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
8: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
8: [----------] 7 tests from FloatingPointDifferenceTest (1 ms total)
8:
8: [----------] 4 tests from FloatingPointToleranceTest
8: [ RUN ] FloatingPointToleranceTest.UlpTolerance
8: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
8: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
8: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
8: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
8: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
8: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
8: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
8: [----------] 4 tests from FloatingPointToleranceTest (0 ms total)
8:
8: [----------] 4 tests from XvgTests
8: [ RUN ] XvgTests.CreateFile
8: [ OK ] XvgTests.CreateFile (2 ms)
8: [ RUN ] XvgTests.CheckMissing
8: [ OK ] XvgTests.CheckMissing (2 ms)
8: [ RUN ] XvgTests.CheckExtra
8: [ OK ] XvgTests.CheckExtra (2 ms)
8: [ RUN ] XvgTests.ReadIncorrect
8: [ OK ] XvgTests.ReadIncorrect (3 ms)
8: [----------] 4 tests from XvgTests (9 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 59 tests from 5 test cases ran. (71 ms total)
8: [ PASSED ] 59 tests.
8/65 Test #8: TestUtilsUnitTests .................... Passed 0.32 sec
test 9
Start 9: TestUtilsMpiUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 1 test from 1 test case.
9: [----------] Global test environment set-up.
9: [----------] 1 test from MpiSelfTest
9: [ RUN ] MpiSelfTest.Runs
9: [ OK ] MpiSelfTest.Runs (1 ms)
9: [----------] 1 test from MpiSelfTest (1 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 1 test from 1 test case ran. (3 ms total)
9: [ PASSED ] 1 test.
9/65 Test #9: TestUtilsMpiUnitTests ................. Passed 0.14 sec
test 10
Start 10: UtilityUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 373 tests from 61 test cases.
10: [----------] Global test environment set-up.
10: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.Move
10: [ OK ] AllocatorTest/0.Move (0 ms)
10: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/0 (1 ms total)
10:
10: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<float, gmx::PageAlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/1.Move
10: [ OK ] AllocatorTest/1.Move (0 ms)
10: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/1 (1 ms total)
10:
10: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.Move
10: [ OK ] AllocatorTest/2.Move (0 ms)
10: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/2 (0 ms total)
10:
10: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.Move
10: [ OK ] AllocatorTest/3.Move (0 ms)
10: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/3 (1 ms total)
10:
10: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/4.Move
10: [ OK ] AllocatorTest/4.Move (0 ms)
10: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/4 (1 ms total)
10:
10: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::PageAlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/5.Move
10: [ OK ] AllocatorTest/5.Move (0 ms)
10: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/5 (1 ms total)
10:
10: [----------] 1 test from AllocatorUntypedTest
10: [ RUN ] AllocatorUntypedTest.Comparison
10: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
10: [----------] 1 test from AllocatorUntypedTest (1 ms total)
10:
10: [----------] 1 test from EmptyArrayRefTest
10: [ RUN ] EmptyArrayRefTest.IsEmpty
10: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
10: [----------] 1 test from EmptyArrayRefTest (0 ms total)
10:
10: [----------] 1 test from EmptyConstArrayRefTest
10: [ RUN ] EmptyConstArrayRefTest.IsEmpty
10: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
10: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
10: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/0 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
10: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (1 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/1 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
10: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/2 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
10: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/3 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
10: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/4 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
10: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/5 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
10: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/6 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
10: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/7 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
10: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/8 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
10: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/9 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
10: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/10 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
10: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/11 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
10: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/12 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
10: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/13 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
10: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/14 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
10: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/15 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
10: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/16 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
10: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/17 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
10: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/18 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
10: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/19 (0 ms total)
10:
10: [----------] 2 tests from CStringUtilityTest
10: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison
10: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms)
10: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength
10: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms)
10: [----------] 2 tests from CStringUtilityTest (0 ms total)
10:
10: [----------] 2 tests from DefaultInitializationAllocator
10: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization
10: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms)
10: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization
10: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms)
10: [----------] 2 tests from DefaultInitializationAllocator (0 ms total)
10:
10: [----------] 4 tests from EnumerationHelpersTest
10: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks
10: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms)
10: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks
10: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms)
10: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe
10: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms)
10: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks
10: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms)
10: [----------] 4 tests from EnumerationHelpersTest (0 ms total)
10:
10: [----------] 9 tests from FixedCapacityVectorTest
10: [ RUN ] FixedCapacityVectorTest.IsEmpty
10: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms)
10: [ RUN ] FixedCapacityVectorTest.PushWorks
10: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.PopWorks
10: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.ClearWorks
10: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks
10: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.AtThrows
10: [ OK ] FixedCapacityVectorTest.AtThrows (1 ms)
10: [ RUN ] FixedCapacityVectorTest.IteratorWorks
10: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks
10: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks
10: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms)
10: [----------] 9 tests from FixedCapacityVectorTest (1 ms total)
10:
10: [----------] 5 tests from InMemorySerializerTest
10: [ RUN ] InMemorySerializerTest.Roundtrip
10: [ OK ] InMemorySerializerTest.Roundtrip (0 ms)
10: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap
10: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms)
10: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap
10: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms)
10: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap
10: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms)
10: [ RUN ] InMemorySerializerTest.SizeIsCorrect
10: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms)
10: [----------] 5 tests from InMemorySerializerTest (0 ms total)
10:
10: [----------] 4 tests from KeyValueTreeSerializerTest
10: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
10: [ OK ] KeyValueTreeSerializerTest.EmptyTree (36 ms)
10: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
10: [ OK ] KeyValueTreeSerializerTest.SimpleObject (1 ms)
10: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
10: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (15 ms)
10: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
10: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (17 ms)
10: [----------] 4 tests from KeyValueTreeSerializerTest (69 ms total)
10:
10: [----------] 6 tests from TreeValueTransformTest
10: [ RUN ] TreeValueTransformTest.SimpleTransforms
10: [ OK ] TreeValueTransformTest.SimpleTransforms (1 ms)
10: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
10: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (1 ms)
10: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
10: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (2 ms)
10: [ RUN ] TreeValueTransformTest.ObjectFromString
10: [ OK ] TreeValueTransformTest.ObjectFromString (1 ms)
10: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
10: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (1 ms)
10: [ RUN ] TreeValueTransformTest.ScopedTransformRules
10: [ OK ] TreeValueTransformTest.ScopedTransformRules (1 ms)
10: [----------] 6 tests from TreeValueTransformTest (7 ms total)
10:
10: [----------] 1 test from TreeValueTransformErrorTest
10: [ RUN ] TreeValueTransformErrorTest.ConversionError
10: [ OK ] TreeValueTransformErrorTest.ConversionError (1 ms)
10: [----------] 1 test from TreeValueTransformErrorTest (1 ms total)
10:
10: [----------] 9 tests from ListOfLists
10: [ RUN ] ListOfLists.EmptyListOfListsWorks
10: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms)
10: [ RUN ] ListOfLists.AppendWorks
10: [ OK ] ListOfLists.AppendWorks (0 ms)
10: [ RUN ] ListOfLists.EmptyListWorks
10: [ OK ] ListOfLists.EmptyListWorks (0 ms)
10: [ RUN ] ListOfLists.AppendAccessWorks
10: [ OK ] ListOfLists.AppendAccessWorks (0 ms)
10: [ RUN ] ListOfLists.ClearWorks
10: [ OK ] ListOfLists.ClearWorks (0 ms)
10: [ RUN ] ListOfLists.OutOfRangeAccessThrows
10: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms)
10: [ RUN ] ListOfLists.FrontAndBackWork
10: [ OK ] ListOfLists.FrontAndBackWork (1 ms)
10: [ RUN ] ListOfLists.ExtractsAndRestores
10: [ OK ] ListOfLists.ExtractsAndRestores (0 ms)
10: [ RUN ] ListOfLists.AppendsListOfListsWithOffset
10: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms)
10: [----------] 9 tests from ListOfLists (1 ms total)
10:
10: [----------] 7 tests from LoggerTest
10: [ RUN ] LoggerTest.EmptyLoggerWorks
10: [ OK ] LoggerTest.EmptyLoggerWorks (1 ms)
10: [ RUN ] LoggerTest.LogsToStream
10: [ OK ] LoggerTest.LogsToStream (0 ms)
10: [ RUN ] LoggerTest.LogsToFile
10: [ OK ] LoggerTest.LogsToFile (2 ms)
10: [ RUN ] LoggerTest.LevelFilteringWorks
10: [ OK ] LoggerTest.LevelFilteringWorks (0 ms)
10: [ RUN ] LoggerTest.LogsToMultipleStreams
10: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms)
10: [ RUN ] LoggerTest.LogsToMultipleFiles
10: [ OK ] LoggerTest.LogsToMultipleFiles (4 ms)
10: [ RUN ] LoggerTest.LogsToStreamAndFile
10: [ OK ] LoggerTest.LogsToStreamAndFile (2 ms)
10: [----------] 7 tests from LoggerTest (10 ms total)
10:
10: [----------] 4 tests from MDModuleNotificationTest
10: [ RUN ] MDModuleNotificationTest.addConsumer
10: [ OK ] MDModuleNotificationTest.addConsumer (0 ms)
10: [ RUN ] MDModuleNotificationTest.addConsumerWithPointerParameter
10: [ OK ] MDModuleNotificationTest.addConsumerWithPointerParameter (0 ms)
10: [ RUN ] MDModuleNotificationTest.addTwoDifferentConsumers
10: [ OK ] MDModuleNotificationTest.addTwoDifferentConsumers (0 ms)
10: [ RUN ] MDModuleNotificationTest.consumerOfTwoResources
10: [ OK ] MDModuleNotificationTest.consumerOfTwoResources (0 ms)
10: [----------] 4 tests from MDModuleNotificationTest (0 ms total)
10:
10: [----------] 4 tests from MutexBasicTest
10: [ RUN ] MutexBasicTest.CanBeMade
10: [ OK ] MutexBasicTest.CanBeMade (0 ms)
10: [ RUN ] MutexBasicTest.CanBeLocked
10: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
10: [ RUN ] MutexBasicTest.CanBeTryLocked
10: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
10: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
10: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
10: [----------] 4 tests from MutexBasicTest (0 ms total)
10:
10: [----------] 3 tests from MutexTaskTest
10: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
10: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (1 ms)
10: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
10: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms)
10: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
10: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
10: [----------] 3 tests from MutexTaskTest (1 ms total)
10:
10: [----------] 2 tests from PathTest
10: [ RUN ] PathTest.StripSourcePrefixWorks
10: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
10: [ RUN ] PathTest.SearchOperationsWork
10: [ OK ] PathTest.SearchOperationsWork (23 ms)
10: [----------] 2 tests from PathTest (23 ms total)
10:
10: [----------] 2 tests from PhysicalNodeCommunicatorTest
10: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
10: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
10: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
10: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
10: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
10:
10: [----------] 5 tests from Range
10: [ RUN ] Range.EmptyRangeWorks
10: [ OK ] Range.EmptyRangeWorks (0 ms)
10: [ RUN ] Range.NonEmptyRangeWorks
10: [ OK ] Range.NonEmptyRangeWorks (0 ms)
10: [ RUN ] Range.BeginEnd
10: [ OK ] Range.BeginEnd (0 ms)
10: [ RUN ] Range.IsInRangeWorks
10: [ OK ] Range.IsInRangeWorks (0 ms)
10: [ RUN ] Range.IteratorWorks
10: [ OK ] Range.IteratorWorks (0 ms)
10: [----------] 5 tests from Range (0 ms total)
10:
10: [----------] 7 tests from StringConvert
10: [ RUN ] StringConvert.NoResultFromEptyString
10: [ OK ] StringConvert.NoResultFromEptyString (0 ms)
10: [ RUN ] StringConvert.ThreeFloatsSuccessfully
10: [ OK ] StringConvert.ThreeFloatsSuccessfully (1 ms)
10: [ RUN ] StringConvert.OneIntSucessfully
10: [ OK ] StringConvert.OneIntSucessfully (0 ms)
10: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows
10: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms)
10: [ RUN ] StringConvert.ThrowsWhenWrongSize
10: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms)
10: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows
10: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms)
10: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay
10: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms)
10: [----------] 7 tests from StringConvert (1 ms total)
10:
10: [----------] 9 tests from StringUtilityTest
10: [ RUN ] StringUtilityTest.StartsWith
10: [ OK ] StringUtilityTest.StartsWith (0 ms)
10: [ RUN ] StringUtilityTest.EndsWith
10: [ OK ] StringUtilityTest.EndsWith (0 ms)
10: [ RUN ] StringUtilityTest.StripSuffixIfPresent
10: [ OK ] StringUtilityTest.StripSuffixIfPresent (1 ms)
10: [ RUN ] StringUtilityTest.StripString
10: [ OK ] StringUtilityTest.StripString (0 ms)
10: [ RUN ] StringUtilityTest.SplitString
10: [ OK ] StringUtilityTest.SplitString (0 ms)
10: [ RUN ] StringUtilityTest.SplitDelimitedString
10: [ OK ] StringUtilityTest.SplitDelimitedString (1 ms)
10: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
10: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms)
10: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive
10: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms)
10: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength
10: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms)
10: [----------] 9 tests from StringUtilityTest (3 ms total)
10:
10: [----------] 2 tests from FormatStringTest
10: [ RUN ] FormatStringTest.HandlesBasicFormatting
10: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
10: [ RUN ] FormatStringTest.HandlesLongStrings
10: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
10: [----------] 2 tests from FormatStringTest (0 ms total)
10:
10: [----------] 1 test from StringFormatterTest
10: [ RUN ] StringFormatterTest.HandlesBasicFormatting
10: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
10: [----------] 1 test from StringFormatterTest (0 ms total)
10:
10: [----------] 1 test from formatAndJoinTest
10: [ RUN ] formatAndJoinTest.Works
10: [ OK ] formatAndJoinTest.Works (0 ms)
10: [----------] 1 test from formatAndJoinTest (0 ms total)
10:
10: [----------] 1 test from JoinStringsTest
10: [ RUN ] JoinStringsTest.Works
10: [ OK ] JoinStringsTest.Works (0 ms)
10: [----------] 1 test from JoinStringsTest (1 ms total)
10:
10: [----------] 6 tests from ReplaceAllTest
10: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
10: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesNoMatches
10: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
10: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
10: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
10: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
10: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
10: [----------] 6 tests from ReplaceAllTest (0 ms total)
10:
10: [----------] 10 tests from TextLineWrapperTest
10: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
10: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
10: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
10: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms)
10: [ RUN ] TextLineWrapperTest.WrapsCorrectly
10: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms)
10: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
10: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (1 ms)
10: [ RUN ] TextLineWrapperTest.HandlesIndent
10: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
10: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (1 ms)
10: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
10: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
10: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms)
10: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
10: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (1 ms)
10: [----------] 10 tests from TextLineWrapperTest (5 ms total)
10:
10: [----------] 1 test from TemplateMPTest
10: [ RUN ] TemplateMPTest.DispatchTemplatedFunction
10: [ OK ] TemplateMPTest.DispatchTemplatedFunction (0 ms)
10: [----------] 1 test from TemplateMPTest (0 ms total)
10:
10: [----------] 6 tests from TextWriterTest
10: [ RUN ] TextWriterTest.WritesLines
10: [ OK ] TextWriterTest.WritesLines (0 ms)
10: [ RUN ] TextWriterTest.WritesLinesInParts
10: [ OK ] TextWriterTest.WritesLinesInParts (1 ms)
10: [ RUN ] TextWriterTest.WritesWrappedLines
10: [ OK ] TextWriterTest.WritesWrappedLines (0 ms)
10: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
10: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (1 ms)
10: [ RUN ] TextWriterTest.TracksNewlines
10: [ OK ] TextWriterTest.TracksNewlines (0 ms)
10: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
10: [ OK ] TextWriterTest.PreservesTrailingWhitespace (1 ms)
10: [----------] 6 tests from TextWriterTest (3 ms total)
10:
10: [----------] 1 test from TypeTraitsTest
10: [ RUN ] TypeTraitsTest.IsIntegralConstant
10: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
10: [----------] 1 test from TypeTraitsTest (0 ms total)
10:
10: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
10: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total)
10:
10: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
10: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (1 ms total)
10:
10: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (1 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
10: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (1 ms total)
10:
10: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
10: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (1 ms total)
10:
10: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (1 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (1 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (1 ms)
10: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (3 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 373 tests from 61 test cases ran. (148 ms total)
10: [ PASSED ] 373 tests.
10/65 Test #10: UtilityUnitTests ...................... Passed 0.29 sec
test 11
Start 11: UtilityMpiUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 2 tests from 1 test case.
11: [----------] Global test environment set-up.
11: [----------] 2 tests from PhysicalNodeCommunicatorTest
11: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
11: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (3 ms)
11: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
11: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (1 ms)
11: [----------] 2 tests from PhysicalNodeCommunicatorTest (4 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 2 tests from 1 test case ran. (5 ms total)
11: [ PASSED ] 2 tests.
11/65 Test #11: UtilityMpiUnitTests ................... Passed 0.22 sec
test 12
Start 12: MdlibUnitTest
12: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdlibUnitTest.xml"
12: Test timeout computed to be: 30
12: [==========] Running 141 tests from 15 test cases.
12: [----------] Global test environment set-up.
12: [----------] 1 test from VerletBufferConstraintTest
12: [ RUN ] VerletBufferConstraintTest.EqualMasses
12: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms)
12: [----------] 1 test from VerletBufferConstraintTest (0 ms total)
12:
12: [----------] 2 tests from PrEbinTest
12: [ RUN ] PrEbinTest.HandlesAverages
12: [ OK ] PrEbinTest.HandlesAverages (57 ms)
12: [ RUN ] PrEbinTest.HandlesEmptyAverages
12: [ OK ] PrEbinTest.HandlesEmptyAverages (1 ms)
12: [----------] 2 tests from PrEbinTest (59 ms total)
12:
12: [----------] 3 tests from EnergyDriftTracker
12: [ RUN ] EnergyDriftTracker.emptyWorks
12: [ OK ] EnergyDriftTracker.emptyWorks (0 ms)
12: [ RUN ] EnergyDriftTracker.onePointWorks
12: [ OK ] EnergyDriftTracker.onePointWorks (0 ms)
12: [ RUN ] EnergyDriftTracker.manyPointsWorks
12: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms)
12: [----------] 3 tests from EnergyDriftTracker (0 ms total)
12:
12: [----------] 4 tests from ShakeTest
12: [ RUN ] ShakeTest.ConstrainsOneBond
12: [ OK ] ShakeTest.ConstrainsOneBond (0 ms)
12: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
12: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
12: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
12: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms)
12: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
12: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
12: [----------] 4 tests from ShakeTest (1 ms total)
12:
12: [----------] 1 test from NullSignalTest
12: [ RUN ] NullSignalTest.NullSignallerWorks
12: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
12: [----------] 1 test from NullSignalTest (0 ms total)
12:
12: [----------] 7 tests from SignalTest
12: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
12: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
12: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
12: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
12: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
12: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
12: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
12: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
12: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
12: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
12: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
12: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
12: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
12: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
12: [----------] 7 tests from SignalTest (1 ms total)
12:
12: [----------] 9 tests from UpdateGroups
12: [ RUN ] UpdateGroups.ethaneUA
12: [ OK ] UpdateGroups.ethaneUA (0 ms)
12: [ RUN ] UpdateGroups.methane
12: [ OK ] UpdateGroups.methane (1 ms)
12: [ RUN ] UpdateGroups.ethane
12: [ OK ] UpdateGroups.ethane (0 ms)
12: [ RUN ] UpdateGroups.butaneUA
12: [ OK ] UpdateGroups.butaneUA (0 ms)
12: [ RUN ] UpdateGroups.waterThreeSite
12: [ OK ] UpdateGroups.waterThreeSite (0 ms)
12: [ RUN ] UpdateGroups.waterFourSite
12: [ OK ] UpdateGroups.waterFourSite (0 ms)
12: [ RUN ] UpdateGroups.fourAtomsWithSettle
12: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
12: [ RUN ] UpdateGroups.waterFlexAngle
12: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
12: [ RUN ] UpdateGroups.twoMoltypes
12: [ OK ] UpdateGroups.twoMoltypes (0 ms)
12: [----------] 9 tests from UpdateGroups (3 ms total)
12:
12: [----------] 1 test from UpdateGroupsCog
12: [ RUN ] UpdateGroupsCog.ComputesCogs
12: [ OK ] UpdateGroupsCog.ComputesCogs (25 ms)
12: [----------] 1 test from UpdateGroupsCog (26 ms total)
12:
12: [----------] 12 tests from WithParameters/ConstraintsTest
12: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0
12: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1
12: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0
12: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1
12: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms)
12: [----------] 12 tests from WithParameters/ConstraintsTest (7 ms total)
12:
12: [----------] 11 tests from WithParameters/EnergyOutputTest
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (18 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (9 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (14 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3
12: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (3 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file
12:
Reading energy frame 0 time 10.100
Reading energy frame 1 time 27.500
Reading energy frame 2 time 44.900
Reading energy frame 3 time 62.300
Reading energy frame 4 time 79.700
Reading energy frame 5 time 97.100
Reading energy frame 6 time 114.500
Reading energy frame 7 time 131.900
Reading energy frame 8 time 149.300
Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (52 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (15 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (14 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (15 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (14 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (13 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (15 ms)
12: [----------] 11 tests from WithParameters/EnergyOutputTest (208 ms total)
12:
12: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (1 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (1 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms)
12: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (8 ms total)
12:
12: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms)
12: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (3 ms total)
12:
12: [----------] 23 tests from WithParameters/FreeEnergyParameterTest
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (1 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (1 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms)
12: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (8 ms total)
12:
12: [----------] 16 tests from WithParameters/LeapFrogTest
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (2 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (12 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (34 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (2 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (13 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (12 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (12 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (13 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (17 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (13 ms)
12: [----------] 16 tests from WithParameters/LeapFrogTest (162 ms total)
12:
12: [----------] 13 tests from WithParameters/SettleTest
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (2 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (2 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (3 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (3 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (14 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (4 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (8 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (18 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (5 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (9 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (9 ms)
12: [----------] 13 tests from WithParameters/SettleTest (88 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 141 tests from 15 test cases ran. (583 ms total)
12: [ PASSED ] 141 tests.
12/65 Test #12: MdlibUnitTest ......................... Passed 1.48 sec
test 13
Start 13: AwhTest
13: Test command: /<<PKGBUILDDIR>>/build/basic/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AwhTest.xml"
13: Test timeout computed to be: 30
13: [==========] Running 17 tests from 6 test cases.
13: [----------] Global test environment set-up.
13: [----------] 1 test from BiasTest
13: [ RUN ] BiasTest.DetectsCovering
13: [ OK ] BiasTest.DetectsCovering (3 ms)
13: [----------] 1 test from BiasTest (3 ms total)
13:
13: [----------] 1 test from biasGridTest
13: [ RUN ] biasGridTest.neighborhood
13: [ OK ] biasGridTest.neighborhood (9 ms)
13: [----------] 1 test from biasGridTest (9 ms total)
13:
13: [----------] 1 test from BiasFepLambdaStateTest
13: [ RUN ] BiasFepLambdaStateTest.DetectsCovering
13: [ OK ] BiasFepLambdaStateTest.DetectsCovering (18 ms)
13: [----------] 1 test from BiasFepLambdaStateTest (18 ms total)
13:
13: [----------] 8 tests from WithParameters/BiasTest
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (42 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (32 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (3 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (3 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (2 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (2 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (3 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (3 ms)
13: [----------] 8 tests from WithParameters/BiasTest (93 ms total)
13:
13: [----------] 2 tests from WithParameters/BiasStateTest
13: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
13: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (2 ms)
13: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
13: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms)
13: [----------] 2 tests from WithParameters/BiasStateTest (3 ms total)
13:
13: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (39 ms)
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (50 ms)
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (45 ms)
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (39 ms)
13: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (184 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 17 tests from 6 test cases ran. (311 ms total)
13: [ PASSED ] 17 tests.
13/65 Test #13: AwhTest ............................... Passed 0.53 sec
test 14
Start 14: DensityFittingAppliedForcesUnitTest
14: Test command: /<<PKGBUILDDIR>>/build/basic/bin/density_fitting_applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml"
14: Test timeout computed to be: 30
14: [==========] Running 18 tests from 4 test cases.
14: [----------] Global test environment set-up.
14: [----------] 2 tests from DensityFittingTest
14: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows
14: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (3 ms)
14: [ RUN ] DensityFittingTest.SingleAtom
14: [ OK ] DensityFittingTest.SingleAtom (44 ms)
14: [----------] 2 tests from DensityFittingTest (48 ms total)
14:
14: [----------] 7 tests from DensityFittingAmplitudeLookupTest
14: [ RUN ] DensityFittingAmplitudeLookupTest.Unity
14: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.Charge
14: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.Masses
14: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign
14: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct
14: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign
14: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct
14: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms)
14: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total)
14:
14: [----------] 1 test from DensityFittingForceProviderState
14: [ RUN ] DensityFittingForceProviderState.RoundTripSaving
14: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms)
14: [----------] 1 test from DensityFittingForceProviderState (0 ms total)
14:
14: [----------] 8 tests from DensityFittingOptionsTest
14: [ RUN ] DensityFittingOptionsTest.DefaultParameters
14: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms)
14: [ RUN ] DensityFittingOptionsTest.OptionSetsActive
14: [ OK ] DensityFittingOptionsTest.OptionSetsActive (1 ms)
14: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive
14: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (1 ms)
14: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive
14: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (1 ms)
14: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup
14: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (1 ms)
14: [ RUN ] DensityFittingOptionsTest.InternalsToKvt
14: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms)
14: [ RUN ] DensityFittingOptionsTest.KvtToInternal
14: [ OK ] DensityFittingOptionsTest.KvtToInternal (1 ms)
14: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent
14: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (1 ms)
14: [----------] 8 tests from DensityFittingOptionsTest (6 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 18 tests from 4 test cases ran. (54 ms total)
14: [ PASSED ] 18 tests.
14/65 Test #14: DensityFittingAppliedForcesUnitTest ... Passed 0.20 sec
test 15
Start 15: AppliedForcesUnitTest
15: Test command: /<<PKGBUILDDIR>>/build/basic/bin/applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml"
15: Test timeout computed to be: 30
15: [==========] Running 3 tests from 1 test case.
15: [----------] Global test environment set-up.
15: [----------] 3 tests from ElectricFieldTest
15: [ RUN ] ElectricFieldTest.Static
15: [ OK ] ElectricFieldTest.Static (2 ms)
15: [ RUN ] ElectricFieldTest.Oscillating
15: [ OK ] ElectricFieldTest.Oscillating (0 ms)
15: [ RUN ] ElectricFieldTest.Pulsed
15: [ OK ] ElectricFieldTest.Pulsed (1 ms)
15: [----------] 3 tests from ElectricFieldTest (3 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 3 tests from 1 test case ran. (3 ms total)
15: [ PASSED ] 3 tests.
15/65 Test #15: AppliedForcesUnitTest ................. Passed 0.10 sec
test 16
Start 16: ListedForcesTest
16: Test command: /<<PKGBUILDDIR>>/build/basic/bin/listed_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/ListedForcesTest.xml"
16: Test timeout computed to be: 30
16: [==========] Running 111 tests from 7 test cases.
16: [----------] Global test environment set-up.
16: [----------] 24 tests from Bond/ListedForcesTest
16: [ RUN ] Bond/ListedForcesTest.Ifunc/0
16: [ OK ] Bond/ListedForcesTest.Ifunc/0 (41 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/1
16: [ OK ] Bond/ListedForcesTest.Ifunc/1 (2 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/2
16: [ OK ] Bond/ListedForcesTest.Ifunc/2 (2 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/3
16: [ OK ] Bond/ListedForcesTest.Ifunc/3 (32 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/4
16: [ OK ] Bond/ListedForcesTest.Ifunc/4 (3 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/5
16: [ OK ] Bond/ListedForcesTest.Ifunc/5 (23 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/6
16: [ OK ] Bond/ListedForcesTest.Ifunc/6 (2 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/7
16: [ OK ] Bond/ListedForcesTest.Ifunc/7 (2 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/8
16: [ OK ] Bond/ListedForcesTest.Ifunc/8 (2 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/9
16: [ OK ] Bond/ListedForcesTest.Ifunc/9 (2 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/10
16: [ OK ] Bond/ListedForcesTest.Ifunc/10 (3 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/11
16: [ OK ] Bond/ListedForcesTest.Ifunc/11 (3 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/12
16: [ OK ] Bond/ListedForcesTest.Ifunc/12 (2 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/13
16: [ OK ] Bond/ListedForcesTest.Ifunc/13 (2 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/14
16: [ OK ] Bond/ListedForcesTest.Ifunc/14 (2 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/15
16: [ OK ] Bond/ListedForcesTest.Ifunc/15 (3 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/16
16: [ OK ] Bond/ListedForcesTest.Ifunc/16 (3 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/17
16: [ OK ] Bond/ListedForcesTest.Ifunc/17 (3 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/18
16: [ OK ] Bond/ListedForcesTest.Ifunc/18 (2 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/19
16: [ OK ] Bond/ListedForcesTest.Ifunc/19 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/20
16: [ OK ] Bond/ListedForcesTest.Ifunc/20 (2 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/21
16: [ OK ] Bond/ListedForcesTest.Ifunc/21 (2 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/22
16: [ OK ] Bond/ListedForcesTest.Ifunc/22 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/23
16: [ OK ] Bond/ListedForcesTest.Ifunc/23 (2 ms)
16: [----------] 24 tests from Bond/ListedForcesTest (148 ms total)
16:
16: [----------] 33 tests from Angle/ListedForcesTest
16: [ RUN ] Angle/ListedForcesTest.Ifunc/0
16: [ OK ] Angle/ListedForcesTest.Ifunc/0 (3 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/1
16: [ OK ] Angle/ListedForcesTest.Ifunc/1 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/2
16: [ OK ] Angle/ListedForcesTest.Ifunc/2 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/3
16: [ OK ] Angle/ListedForcesTest.Ifunc/3 (23 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/4
16: [ OK ] Angle/ListedForcesTest.Ifunc/4 (3 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/5
16: [ OK ] Angle/ListedForcesTest.Ifunc/5 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/6
16: [ OK ] Angle/ListedForcesTest.Ifunc/6 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/7
16: [ OK ] Angle/ListedForcesTest.Ifunc/7 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/8
16: [ OK ] Angle/ListedForcesTest.Ifunc/8 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/9
16: [ OK ] Angle/ListedForcesTest.Ifunc/9 (3 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/10
16: [ OK ] Angle/ListedForcesTest.Ifunc/10 (3 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/11
16: [ OK ] Angle/ListedForcesTest.Ifunc/11 (3 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/12
16: [ OK ] Angle/ListedForcesTest.Ifunc/12 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/13
16: [ OK ] Angle/ListedForcesTest.Ifunc/13 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/14
16: [ OK ] Angle/ListedForcesTest.Ifunc/14 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/15
16: [ OK ] Angle/ListedForcesTest.Ifunc/15 (3 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/16
16: [ OK ] Angle/ListedForcesTest.Ifunc/16 (3 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/17
16: [ OK ] Angle/ListedForcesTest.Ifunc/17 (3 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/18
16: [ OK ] Angle/ListedForcesTest.Ifunc/18 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/19
16: [ OK ] Angle/ListedForcesTest.Ifunc/19 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/20
16: [ OK ] Angle/ListedForcesTest.Ifunc/20 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/21
16: [ OK ] Angle/ListedForcesTest.Ifunc/21 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/22
16: [ OK ] Angle/ListedForcesTest.Ifunc/22 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/23
16: [ OK ] Angle/ListedForcesTest.Ifunc/23 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/24
16: [ OK ] Angle/ListedForcesTest.Ifunc/24 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/25
16: [ OK ] Angle/ListedForcesTest.Ifunc/25 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/26
16: [ OK ] Angle/ListedForcesTest.Ifunc/26 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/27
16: [ OK ] Angle/ListedForcesTest.Ifunc/27 (3 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/28
16: [ OK ] Angle/ListedForcesTest.Ifunc/28 (3 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/29
16: [ OK ] Angle/ListedForcesTest.Ifunc/29 (3 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/30
16: [ OK ] Angle/ListedForcesTest.Ifunc/30 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/31
16: [ OK ] Angle/ListedForcesTest.Ifunc/31 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/32
16: [ OK ] Angle/ListedForcesTest.Ifunc/32 (1 ms)
16: [----------] 33 tests from Angle/ListedForcesTest (97 ms total)
16:
16: [----------] 18 tests from Dihedral/ListedForcesTest
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (4 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (2 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (2 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (2 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (2 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (2 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (2 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (3 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (2 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (2 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (3 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (1 ms)
16: [----------] 18 tests from Dihedral/ListedForcesTest (34 ms total)
16:
16: [----------] 12 tests from Polarize/ListedForcesTest
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/0
16: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/1
16: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/2
16: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/3
16: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/4
16: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/5
16: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/6
16: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/7
16: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/8
16: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/9
16: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/10
16: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/11
16: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (1 ms)
16: [----------] 12 tests from Polarize/ListedForcesTest (13 ms total)
16:
16: [----------] 18 tests from Restraints/ListedForcesTest
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/0
16: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (2 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/1
16: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (2 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/2
16: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (2 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/3
16: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/4
16: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/5
16: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/6
16: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (2 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/7
16: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (2 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/8
16: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (2 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/9
16: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/10
16: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/11
16: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/12
16: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/13
16: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/14
16: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/15
16: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (2 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/16
16: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (3 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/17
16: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (2 ms)
16: [----------] 18 tests from Restraints/ListedForcesTest (31 ms total)
16:
16: [----------] 3 tests from BondZeroLength/ListedForcesTest
16: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0
16: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1
16: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2
16: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (1 ms)
16: [----------] 3 tests from BondZeroLength/ListedForcesTest (3 ms total)
16:
16: [----------] 3 tests from AngleZero/ListedForcesTest
16: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0
16: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1
16: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2
16: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (1 ms)
16: [----------] 3 tests from AngleZero/ListedForcesTest (4 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 111 tests from 7 test cases ran. (330 ms total)
16: [ PASSED ] 111 tests.
16/65 Test #16: ListedForcesTest ...................... Passed 0.48 sec
test 17
Start 17: CommandLineUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/basic/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CommandLineUnitTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 59 tests from 7 test cases.
17: [----------] Global test environment set-up.
17: [----------] 3 tests from CommandLineHelpModuleTest
17: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
17: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (4 ms)
17: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
17: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (14 ms)
17: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
17: [ OK ] CommandLineHelpModuleTest.ExportsHelp (27 ms)
17: [----------] 3 tests from CommandLineHelpModuleTest (45 ms total)
17:
17: [----------] 7 tests from CommandLineHelpWriterTest
17: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
17: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (3 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
17: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
17: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (2 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
17: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
17: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
17: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues
17: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (1 ms)
17: [----------] 7 tests from CommandLineHelpWriterTest (11 ms total)
17:
17: [----------] 6 tests from CommandLineModuleManagerTest
17: [ RUN ] CommandLineModuleManagerTest.RunsModule
17: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (1 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (2 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms)
17: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
17: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (1 ms)
17: [----------] 6 tests from CommandLineModuleManagerTest (5 ms total)
17:
17: [----------] 13 tests from CommandLineParserTest
17: [ RUN ] CommandLineParserTest.HandlesSingleValues
17: [ OK ] CommandLineParserTest.HandlesSingleValues (1 ms)
17: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
17: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
17: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
17: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
17: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (1 ms)
17: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
17: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (1 ms)
17: [ RUN ] CommandLineParserTest.HandlesString
17: [ OK ] CommandLineParserTest.HandlesString (0 ms)
17: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
17: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
17: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
17: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
17: [ OK ] CommandLineParserTest.HandlesSkipUnknown (1 ms)
17: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
17: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms)
17: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
17: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
17: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
17: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (1 ms)
17: [----------] 13 tests from CommandLineParserTest (6 ms total)
17:
17: [----------] 6 tests from CommandLineProgramContextTest
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
17: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (1 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
17: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (1 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (1 ms)
17: [----------] 6 tests from CommandLineProgramContextTest (3 ms total)
17:
17: [----------] 3 tests from OutputNamesTest
17: [ RUN ] OutputNamesTest.CanBeSuffixed
17: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms)
17: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend
17: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms)
17: [ RUN ] OutputNamesTest.CanHavePartNumberAdded
17: [ OK ] OutputNamesTest.CanHavePartNumberAdded (1 ms)
17: [----------] 3 tests from OutputNamesTest (1 ms total)
17:
17: [----------] 21 tests from ParseCommonArgsTest
17: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
17: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
17: [ OK ] ParseCommonArgsTest.ParsesInt64Args (1 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
17: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
17: [ OK ] ParseCommonArgsTest.ParsesStringArgs (1 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
17: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
17: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
17: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (1 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
17: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
17: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (1 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
17: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
17: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
17: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
17: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
17: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
17: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (1 ms)
17: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
17: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (1 ms)
17: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
17: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (1 ms)
17: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
17: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (2 ms)
17: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
17: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms)
17: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
17: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (6 ms)
17: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
17: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (4 ms)
17: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
17: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms)
17: [----------] 21 tests from ParseCommonArgsTest (21 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 59 tests from 7 test cases ran. (94 ms total)
17: [ PASSED ] 59 tests.
17/65 Test #17: CommandLineUnitTests .................. Passed 0.17 sec
test 18
Start 18: DomDecTests
18: Test command: /<<PKGBUILDDIR>>/build/basic/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/DomDecTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 9 tests from 2 test cases.
18: [----------] Global test environment set-up.
18: [----------] 7 tests from HashedMap
18: [ RUN ] HashedMap.InsertsFinds
18: [ OK ] HashedMap.InsertsFinds (0 ms)
18: [ RUN ] HashedMap.NegativeKeysWork
18: [ OK ] HashedMap.NegativeKeysWork (0 ms)
18: [ RUN ] HashedMap.InsertsErases
18: [ OK ] HashedMap.InsertsErases (0 ms)
18: [ RUN ] HashedMap.InsertsOrAssigns
18: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
18: [ RUN ] HashedMap.Clears
18: [ OK ] HashedMap.Clears (0 ms)
18: [ RUN ] HashedMap.LinkedEntries
18: [ OK ] HashedMap.LinkedEntries (0 ms)
18: [ RUN ] HashedMap.ResizesTable
18: [ OK ] HashedMap.ResizesTable (0 ms)
18: [----------] 7 tests from HashedMap (2 ms total)
18:
18: [----------] 2 tests from LocalAtomSetManager
18: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
18: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms)
18: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
18: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
18: [----------] 2 tests from LocalAtomSetManager (1 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 9 tests from 2 test cases ran. (5 ms total)
18: [ PASSED ] 9 tests.
18/65 Test #18: DomDecTests ........................... Passed 0.18 sec
test 19
Start 19: DomDecMpiTests
19: Test command: /<<PKGBUILDDIR>>/build/basic/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/DomDecMpiTests.xml"
19: Test timeout computed to be: 30
19: [==========] Running 4 tests from 1 test case.
19: [----------] Global test environment set-up.
19: [----------] 4 tests from HaloExchangeTest
19: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse
19: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (3 ms)
19: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses
19: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (4 ms)
19: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim
19: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (8 ms)
19: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1
19: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (1 ms)
19: [----------] 4 tests from HaloExchangeTest (16 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 4 tests from 1 test case ran. (16 ms total)
19: [ PASSED ] 4 tests.
19/65 Test #19: DomDecMpiTests ........................ Passed 0.17 sec
test 20
Start 20: EwaldUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/basic/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EwaldUnitTests.xml"
20: Test timeout computed to be: 30
20: [==========] Running 185 tests from 10 test cases.
20: [----------] Global test environment set-up.
20: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (2 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (12 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms)
20: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (16 ms total)
20:
20: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (76 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (42 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (52 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (10 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (10 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (20 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (16 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (9 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (10 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (9 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (29 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (10 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (51 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (25 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (11 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (18 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (12 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (11 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (12 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (11 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (12 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (12 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (12 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (12 ms)
20: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (510 ms total)
20:
20: [----------] 72 tests from SaneInput/PmeGatherTest
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (3 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (3 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (3 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (3 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (3 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (3 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (10 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (3 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (3 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (3 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (2 ms)
20: [----------] 72 tests from SaneInput/PmeGatherTest (158 ms total)
20:
20: [----------] 16 tests from SaneInput/PmeSolveTest
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (7 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (9 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (5 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (9 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (10 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (5 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (5 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (5 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (9 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (5 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (9 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (22 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (3 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (6 ms)
20: [----------] 16 tests from SaneInput/PmeSolveTest (119 ms total)
20:
20: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (5 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (5 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (3 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (3 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (5 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (5 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (3 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (3 ms)
20: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (34 ms total)
20:
20: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (9 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (9 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (6 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (6 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (9 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (9 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (5 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (6 ms)
20: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (59 ms total)
20:
20: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (5 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (9 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (5 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (8 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (6 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (7 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (5 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (9 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (5 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (9 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (4 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (6 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (6 ms)
20: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (96 ms total)
20:
20: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (18 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (14 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (7 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (8 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (9 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (9 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (5 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (6 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (7 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (8 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (9 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (10 ms)
20: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (114 ms total)
20:
20: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (6 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (8 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (8 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (10 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (11 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (13 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (12 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (7 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (9 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (14 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (35 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (16 ms)
20: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (153 ms total)
20:
20: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (18 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (44 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (26 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (54 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (37 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (64 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (17 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (19 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (25 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (28 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (34 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (40 ms)
20: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (434 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 185 tests from 10 test cases ran. (1693 ms total)
20: [ PASSED ] 185 tests.
20/65 Test #20: EwaldUnitTests ........................ Passed 1.90 sec
test 21
Start 21: FFTUnitTests
21: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FFTUnitTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 14 tests from 4 test cases.
21: [----------] Global test environment set-up.
21: [----------] 2 tests from ManyFFTTest
21: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
21: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (90 ms)
21: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
21: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (79 ms)
21: [----------] 2 tests from ManyFFTTest (174 ms total)
21:
21: [----------] 1 test from FFTTest
21: [ RUN ] FFTTest.Real2DLength18_15Test
21: [ OK ] FFTTest.Real2DLength18_15Test (56 ms)
21: [----------] 1 test from FFTTest (57 ms total)
21:
21: [----------] 1 test from FFFTest3D
21: [ RUN ] FFFTest3D.Real5_6_9
21: [ OK ] FFFTest3D.Real5_6_9 (13 ms)
21: [----------] 1 test from FFFTest3D (15 ms total)
21:
21: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (4 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (3 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (6 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (12 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (9 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (3 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (3 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (4 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (31 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (44 ms)
21: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (124 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 14 tests from 4 test cases ran. (371 ms total)
21: [ PASSED ] 14 tests.
21/65 Test #21: FFTUnitTests .......................... Passed 0.54 sec
test 22
Start 22: GpuUtilsUnitTests
22: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 64 tests from 22 test cases.
22: [----------] Global test environment set-up.
22: [----------] 2 tests from ClfftInitializer
22: [ RUN ] ClfftInitializer.SingleInitializationWorks
22: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms)
22: [ RUN ] ClfftInitializer.TwoInitializationsWork
22: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms)
22: [----------] 2 tests from ClfftInitializer (0 ms total)
22:
22: [----------] 1 test from DevicesAvailable
22: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice
22: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms)
22: [----------] 1 test from DevicesAvailable (0 ms total)
22:
22: [----------] 1 test from DeviceStreamManagerTest
22: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice
22: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms)
22: [----------] 1 test from DeviceStreamManagerTest (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
22: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/0 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float
22: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/1 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<float>
22: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
22: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/3 (0 ms total)
22:
22: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
22: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
22: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
22: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
22: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
22: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total)
22:
22: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float
22: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
22: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
22: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
22: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
22: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total)
22:
22: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<float>
22: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
22: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
22: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
22: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
22: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
22: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
22: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.Swap
22: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.Comparison
22: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float
22: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
22: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.Swap
22: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.Comparison
22: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/1 (1 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<float>
22: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
22: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.Swap
22: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.Comparison
22: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
22: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
22: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.Swap
22: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.Comparison
22: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
22: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
22: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
22: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float
22: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
22: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
22: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (1 ms total)
22:
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<float>
22: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
22: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
22: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total)
22:
22: [----------] 1 test from HostAllocatorUntypedTest
22: [ RUN ] HostAllocatorUntypedTest.Comparison
22: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
22: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
22:
22: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (1 ms)
22: [ RUN ] AllocatorTest/0.Move
22: [ OK ] AllocatorTest/0.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/0 (1 ms total)
22:
22: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/1.Move
22: [ OK ] AllocatorTest/1.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/1 (0 ms total)
22:
22: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms)
22: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (1 ms)
22: [ RUN ] AllocatorTest/2.Move
22: [ OK ] AllocatorTest/2.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/2 (2 ms total)
22:
22: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/3.Move
22: [ OK ] AllocatorTest/3.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/3 (0 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 64 tests from 22 test cases ran. (7 ms total)
22: [ PASSED ] 64 tests.
22/65 Test #22: GpuUtilsUnitTests ..................... Passed 0.12 sec
test 23
Start 23: HardwareUnitTests
23: Test command: /<<PKGBUILDDIR>>/build/basic/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/HardwareUnitTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 6 tests from 3 test cases.
23: [----------] Global test environment set-up.
23: [----------] 1 test from CpuInfoTest
23: [ RUN ] CpuInfoTest.SupportLevel
23: [ OK ] CpuInfoTest.SupportLevel (2 ms)
23: [----------] 1 test from CpuInfoTest (2 ms total)
23:
23: [----------] 4 tests from HardwareTopologyTest
23: [ RUN ] HardwareTopologyTest.Execute
23: [ OK ] HardwareTopologyTest.Execute (36 ms)
23: [ RUN ] HardwareTopologyTest.HwlocExecute
23: [ OK ] HardwareTopologyTest.HwlocExecute (34 ms)
23: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
23: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (33 ms)
23: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
23: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (33 ms)
23: [----------] 4 tests from HardwareTopologyTest (139 ms total)
23:
23: [----------] 1 test from DevicesManagerTest
23: [ RUN ] DevicesManagerTest.Serialization
23: [ OK ] DevicesManagerTest.Serialization (0 ms)
23: [----------] 1 test from DevicesManagerTest (0 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 6 tests from 3 test cases ran. (142 ms total)
23: [ PASSED ] 6 tests.
23/65 Test #23: HardwareUnitTests ..................... Passed 0.26 sec
test 24
Start 24: MathUnitTests
24: Test command: /<<PKGBUILDDIR>>/build/basic/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MathUnitTests.xml"
24: Test timeout computed to be: 30
24: [==========] Running 292 tests from 32 test cases.
24: [----------] Global test environment set-up.
24: [----------] 1 test from EmptyArrayRefWithPaddingTest
24: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
24: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
24: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total)
24:
24: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
24: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
24: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
24: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (1 ms total)
24:
24: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
24: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
24: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
24: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
24: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
24: [----------] 2 tests from ArrayRefWithPaddingTest/0 (1 ms total)
24:
24: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
24: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
24: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
24: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
24: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
24: [----------] 2 tests from ArrayRefWithPaddingTest/1 (1 ms total)
24:
24: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
24: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
24: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
24: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
24: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
24: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total)
24:
24: [----------] 11 tests from TranslateAndScaleTest
24: [ RUN ] TranslateAndScaleTest.identityTransformation
24: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms)
24: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling
24: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation
24: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms)
24: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial
24: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms)
24: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector
24: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingIdentity
24: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingNonTrivial
24: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector
24: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero
24: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (1 ms)
24: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero
24: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector
24: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms)
24: [----------] 11 tests from TranslateAndScaleTest (4 ms total)
24:
24: [----------] 2 tests from AffineTransformationTest
24: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors
24: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms)
24: [ RUN ] AffineTransformationTest.applyTransformationToVectors
24: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms)
24: [----------] 2 tests from AffineTransformationTest (0 ms total)
24:
24: [----------] 12 tests from DensitySimilarityTest
24: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect
24: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect
24: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch
24: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms)
24: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch
24: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms)
24: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect
24: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero
24: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms)
24: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect
24: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect
24: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (16 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne
24: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (122 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated
24: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (133 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated
24: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (117 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect
24: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (2 ms)
24: [----------] 12 tests from DensitySimilarityTest (394 ms total)
24:
24: [----------] 6 tests from StructureSimilarityTest
24: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
24: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
24: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
24: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
24: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
24: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
24: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
24: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
24: [----------] 6 tests from StructureSimilarityTest (2 ms total)
24:
24: [----------] 8 tests from ExponentialMovingAverage
24: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero
24: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms)
24: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative
24: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms)
24: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue
24: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms)
24: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue
24: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms)
24: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly
24: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms)
24: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing
24: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms)
24: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect
24: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms)
24: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree
24: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms)
24: [----------] 8 tests from ExponentialMovingAverage (3 ms total)
24:
24: [----------] 21 tests from FunctionTest
24: [ RUN ] FunctionTest.StaticLog2
24: [ OK ] FunctionTest.StaticLog2 (1 ms)
24: [ RUN ] FunctionTest.Log2I32Bit
24: [ OK ] FunctionTest.Log2I32Bit (1 ms)
24: [ RUN ] FunctionTest.Log2I64Bit
24: [ OK ] FunctionTest.Log2I64Bit (1 ms)
24: [ RUN ] FunctionTest.GreatestCommonDivisor
24: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
24: [ RUN ] FunctionTest.InvsqrtFloat
24: [ OK ] FunctionTest.InvsqrtFloat (1 ms)
24: [ RUN ] FunctionTest.InvsqrtDouble
24: [ OK ] FunctionTest.InvsqrtDouble (1 ms)
24: [ RUN ] FunctionTest.InvsqrtInteger
24: [ OK ] FunctionTest.InvsqrtInteger (1 ms)
24: [ RUN ] FunctionTest.InvcbrtFloat
24: [ OK ] FunctionTest.InvcbrtFloat (1 ms)
24: [ RUN ] FunctionTest.InvcbrtDouble
24: [ OK ] FunctionTest.InvcbrtDouble (1 ms)
24: [ RUN ] FunctionTest.InvcbrtInteger
24: [ OK ] FunctionTest.InvcbrtInteger (0 ms)
24: [ RUN ] FunctionTest.SixthrootFloat
24: [ OK ] FunctionTest.SixthrootFloat (0 ms)
24: [ RUN ] FunctionTest.SixthrootDouble
24: [ OK ] FunctionTest.SixthrootDouble (0 ms)
24: [ RUN ] FunctionTest.SixthrootInteger
24: [ OK ] FunctionTest.SixthrootInteger (1 ms)
24: [ RUN ] FunctionTest.InvsixthrootFloat
24: [ OK ] FunctionTest.InvsixthrootFloat (1 ms)
24: [ RUN ] FunctionTest.InvsixthrootDouble
24: [ OK ] FunctionTest.InvsixthrootDouble (1 ms)
24: [ RUN ] FunctionTest.InvsixthrootInteger
24: [ OK ] FunctionTest.InvsixthrootInteger (1 ms)
24: [ RUN ] FunctionTest.Powers
24: [ OK ] FunctionTest.Powers (0 ms)
24: [ RUN ] FunctionTest.ErfInvFloat
24: [ OK ] FunctionTest.ErfInvFloat (1 ms)
24: [ RUN ] FunctionTest.ErfInvDouble
24: [ OK ] FunctionTest.ErfInvDouble (1 ms)
24: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
24: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (1 ms)
24: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
24: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms)
24: [----------] 21 tests from FunctionTest (20 ms total)
24:
24: [----------] 4 tests from GaussianOn1DLattice
24: [ RUN ] GaussianOn1DLattice.sumsCloseToOne
24: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms)
24: [ RUN ] GaussianOn1DLattice.isCorrect
24: [ OK ] GaussianOn1DLattice.isCorrect (0 ms)
24: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero
24: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (1 ms)
24: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange
24: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms)
24: [----------] 4 tests from GaussianOn1DLattice (2 ms total)
24:
24: [----------] 9 tests from GaussTransformTest
24: [ RUN ] GaussTransformTest.isZeroUponConstruction
24: [ OK ] GaussTransformTest.isZeroUponConstruction (1 ms)
24: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss
24: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms)
24: [ RUN ] GaussTransformTest.isZeroAfterSettingZero
24: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms)
24: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX
24: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms)
24: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY
24: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms)
24: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ
24: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms)
24: [ RUN ] GaussTransformTest.complementaryGaussAddToZero
24: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms)
24: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues
24: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (1 ms)
24: [ RUN ] GaussTransformTest.view
24: [ OK ] GaussTransformTest.view (0 ms)
24: [----------] 9 tests from GaussTransformTest (3 ms total)
24:
24: [----------] 3 tests from DensityFittingForce
24: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity
24: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms)
24: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections
24: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms)
24: [ RUN ] DensityFittingForce.pullsTowardsDerivative
24: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms)
24: [----------] 3 tests from DensityFittingForce (1 ms total)
24:
24: [----------] 2 tests from InvertMatrixTest
24: [ RUN ] InvertMatrixTest.IdentityIsImpotent
24: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
24: [ RUN ] InvertMatrixTest.ComputesInverse
24: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
24: [----------] 2 tests from InvertMatrixTest (0 ms total)
24:
24: [----------] 2 tests from InvertBoxMatrixTest
24: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
24: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
24: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
24: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
24: [----------] 2 tests from InvertBoxMatrixTest (0 ms total)
24:
24: [----------] 17 tests from MatrixTest
24: [ RUN ] MatrixTest.canSetFromArray
24: [ OK ] MatrixTest.canSetFromArray (0 ms)
24: [ RUN ] MatrixTest.canSetStaticallyFromList
24: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms)
24: [ RUN ] MatrixTest.canConstructAndFill
24: [ OK ] MatrixTest.canConstructAndFill (0 ms)
24: [ RUN ] MatrixTest.canSetValues
24: [ OK ] MatrixTest.canSetValues (0 ms)
24: [ RUN ] MatrixTest.canCopyAssign
24: [ OK ] MatrixTest.canCopyAssign (0 ms)
24: [ RUN ] MatrixTest.canSwap
24: [ OK ] MatrixTest.canSwap (0 ms)
24: [ RUN ] MatrixTest.staticMultiDimArrayExtent
24: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms)
24: [ RUN ] MatrixTest.determinantWorks
24: [ OK ] MatrixTest.determinantWorks (0 ms)
24: [ RUN ] MatrixTest.noninvertableDeterminantIsZero
24: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms)
24: [ RUN ] MatrixTest.determinantOfDiagonalMatrix
24: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms)
24: [ RUN ] MatrixTest.traceWorks
24: [ OK ] MatrixTest.traceWorks (0 ms)
24: [ RUN ] MatrixTest.transposeWorks
24: [ OK ] MatrixTest.transposeWorks (0 ms)
24: [ RUN ] MatrixTest.transposeOfSymmetricMatrix
24: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms)
24: [ RUN ] MatrixTest.canCreateFromLegacyMatrix
24: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms)
24: [ RUN ] MatrixTest.canFillLegacyMatrix
24: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms)
24: [ RUN ] MatrixTest.IdentityMatrix
24: [ OK ] MatrixTest.IdentityMatrix (1 ms)
24: [ RUN ] MatrixTest.MatrixVectorMultiplication
24: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms)
24: [----------] 17 tests from MatrixTest (4 ms total)
24:
24: [----------] 25 tests from MultiDimArrayTest
24: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic
24: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic
24: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSetValuesInStatic
24: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic
24: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveConstructStatic
24: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic
24: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveAssignStatic
24: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic
24: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyConstructStatic
24: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic
24: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyAssignStatic
24: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic
24: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSwapStatic
24: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSwapDynamic
24: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent
24: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms)
24: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent
24: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms)
24: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent
24: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms)
24: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue
24: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms)
24: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray
24: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (1 ms)
24: [ RUN ] MultiDimArrayTest.conversionToView
24: [ OK ] MultiDimArrayTest.conversionToView (0 ms)
24: [ RUN ] MultiDimArrayTest.conversionToConstView
24: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms)
24: [ RUN ] MultiDimArrayTest.viewBegin
24: [ OK ] MultiDimArrayTest.viewBegin (0 ms)
24: [ RUN ] MultiDimArrayTest.viewEnd
24: [ OK ] MultiDimArrayTest.viewEnd (0 ms)
24: [ RUN ] MultiDimArrayTest.constViewConstBegin
24: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms)
24: [ RUN ] MultiDimArrayTest.constViewConstEnd
24: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms)
24: [----------] 25 tests from MultiDimArrayTest (1 ms total)
24:
24: [----------] 4 tests from MultiDimArrayToMdSpanTest
24: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms)
24: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms)
24: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms)
24: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms)
24: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total)
24:
24: [----------] 9 tests from NelderMeadSimplexTest
24: [ RUN ] NelderMeadSimplexTest.BestVertex
24: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms)
24: [ RUN ] NelderMeadSimplexTest.WorstVertex
24: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms)
24: [ RUN ] NelderMeadSimplexTest.SecondWorstValue
24: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms)
24: [ RUN ] NelderMeadSimplexTest.ReflectionPoint
24: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms)
24: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint
24: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms)
24: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint
24: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms)
24: [ RUN ] NelderMeadSimplexTest.SwapOutWorst
24: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms)
24: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest
24: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms)
24: [ RUN ] NelderMeadSimplexTest.OrientedLength
24: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms)
24: [----------] 9 tests from NelderMeadSimplexTest (1 ms total)
24:
24: [----------] 2 tests from NelderMead
24: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly
24: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms)
24: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly
24: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (1 ms)
24: [----------] 2 tests from NelderMead (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
24: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ResizeWorks
24: [ OK ] PaddedVectorTest/0.ResizeWorks (1 ms)
24: [ RUN ] PaddedVectorTest/0.ReserveWorks
24: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/0.CanCopyAssign
24: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/0.CanMoveAssign
24: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/0.CanSwap
24: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/0 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
24: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ResizeWorks
24: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ReserveWorks
24: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/1.CanCopyAssign
24: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/1.CanMoveAssign
24: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/1.CanSwap
24: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/1 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
24: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ResizeWorks
24: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ReserveWorks
24: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/2.CanCopyAssign
24: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/2.CanMoveAssign
24: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/2.CanSwap
24: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/2 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
24: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ResizeWorks
24: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ReserveWorks
24: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/3.CanCopyAssign
24: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/3.CanMoveAssign
24: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/3.CanSwap
24: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/3 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
24: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ResizeWorks
24: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ReserveWorks
24: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/4.CanCopyAssign
24: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/4.CanMoveAssign
24: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/4.CanSwap
24: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/4 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ResizeWorks
24: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ReserveWorks
24: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/5.CanCopyAssign
24: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/5.CanMoveAssign
24: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/5.CanSwap
24: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/5 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ResizeWorks
24: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ReserveWorks
24: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/6.CanCopyAssign
24: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/6.CanMoveAssign
24: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/6.CanSwap
24: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/6 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ResizeWorks
24: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ReserveWorks
24: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/7.CanCopyAssign
24: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/7.CanMoveAssign
24: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/7.CanSwap
24: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/7 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ResizeWorks
24: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ReserveWorks
24: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/8.CanCopyAssign
24: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/8.CanMoveAssign
24: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/8.CanSwap
24: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/8 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ResizeWorks
24: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ReserveWorks
24: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (1 ms)
24: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/9.CanCopyAssign
24: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/9.CanMoveAssign
24: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/9.CanSwap
24: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/9 (1 ms total)
24:
24: [----------] 37 tests from RVecTest
24: [ RUN ] RVecTest.CanBeStoredInVector
24: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
24: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
24: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
24: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
24: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
24: [ RUN ] RVecTest.WorksAsMutable_rvec
24: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
24: [ RUN ] RVecTest.WorksAs_rvec_Array
24: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
24: [ RUN ] RVecTest.CanAddRVecToRvec
24: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
24: [ RUN ] RVecTest.CanAddAssignRVecToRvec
24: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
24: [ RUN ] RVecTest.CanSubtractRVecFromRvec
24: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
24: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
24: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
24: [ RUN ] RVecTest.CanDotProductRVecByRvec
24: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
24: [ RUN ] RVecTest.CanCrossProductRVecByRvec
24: [ OK ] RVecTest.CanCrossProductRVecByRvec (1 ms)
24: [ RUN ] RVecTest.CanDivideRVecInplace
24: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
24: [ RUN ] RVecTest.CanScaleRVec
24: [ OK ] RVecTest.CanScaleRVec (0 ms)
24: [ RUN ] RVecTest.CanDivideRVec
24: [ OK ] RVecTest.CanDivideRVec (0 ms)
24: [ RUN ] RVecTest.CanDoUnitvFromRVec
24: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
24: [ RUN ] RVecTest.CanSqLengthOfRVec
24: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanLengthOfRVec
24: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanCastToRVec
24: [ OK ] RVecTest.CanCastToRVec (0 ms)
24: [ RUN ] RVecTest.CanCastToDVec
24: [ OK ] RVecTest.CanCastToDVec (0 ms)
24: [ RUN ] RVecTest.CanLeftScalarMultiply
24: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
24: [ RUN ] RVecTest.CanRightScalarMultiply
24: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
24: [ RUN ] RVecTest.CanGetUnitvFromRVec
24: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
24: [ RUN ] RVecTest.CanGetSqLengthOfRVec
24: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanGetLengthOfRVec
24: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanDoCrossProductOfRVec
24: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
24: [ RUN ] RVecTest.CanDoDotProductOfRVec
24: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
24: [ RUN ] RVecTest.CanScaleByVector
24: [ OK ] RVecTest.CanScaleByVector (0 ms)
24: [ RUN ] RVecTest.asIVec
24: [ OK ] RVecTest.asIVec (0 ms)
24: [ RUN ] RVecTest.elementWiseMin
24: [ OK ] RVecTest.elementWiseMin (0 ms)
24: [ RUN ] RVecTest.elementWiseMax
24: [ OK ] RVecTest.elementWiseMax (0 ms)
24: [ RUN ] RVecTest.WorksAs_dvec_Reference
24: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
24: [ RUN ] RVecTest.WorksAs_ivec_Reference
24: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
24: [ RUN ] RVecTest.WorksAs_rvec_Reference
24: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
24: [ RUN ] RVecTest.CopyConstructorWorks
24: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
24: [ RUN ] RVecTest.CopyAssignmentWorks
24: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
24: [ RUN ] RVecTest.MoveConstructorWorks
24: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
24: [ RUN ] RVecTest.MoveAssignmentWorks
24: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
24: [----------] 37 tests from RVecTest (2 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 292 tests from 32 test cases ran. (456 ms total)
24: [ PASSED ] 292 tests.
24/65 Test #24: MathUnitTests ......................... Passed 0.57 sec
test 25
Start 25: MdrunUtilityUnitTests
25: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml"
25: Test timeout computed to be: 30
25: [==========] Running 17 tests from 1 test case.
25: [----------] Global test environment set-up.
25: [----------] 17 tests from ThreadAffinityTest
25: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
25: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
25: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (2 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (1 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
25: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
25: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
25: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
25: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
25: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
25: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (2 ms)
25: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
25: NOTE: Affinity setting failed.
25: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
25: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
25: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (2 ms)
25: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
25: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (1 ms)
25: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
25: NOTE: Affinity setting for 1/2 threads failed.
25: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (2 ms)
25: [----------] 17 tests from ThreadAffinityTest (17 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 17 tests from 1 test case ran. (18 ms total)
25: [ PASSED ] 17 tests.
25/65 Test #25: MdrunUtilityUnitTests ................. Passed 0.08 sec
test 26
Start 26: MdrunUtilityMpiUnitTests
26: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
26: Test timeout computed to be: 30
26: [==========] Running 13 tests from 2 test cases.
26: [----------] Global test environment set-up.
26: [----------] 6 tests from ThreadAffinityMultiRankTest
26: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
26: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (7 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
26: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (9 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
26: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (5 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
26: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (2 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
26: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (3 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
26: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (3 ms)
26: [----------] 6 tests from ThreadAffinityMultiRankTest (29 ms total)
26:
26: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (5 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (3 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (4 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (4 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (4 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (6 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (4 ms)
26: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (31 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 13 tests from 2 test cases ran. (60 ms total)
26: [ PASSED ] 13 tests.
26/65 Test #26: MdrunUtilityMpiUnitTests .............. Passed 0.13 sec
test 27
Start 27: MDSpanTests
27: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdspan-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MDSpanTests.xml"
27: Test timeout computed to be: 30
27: [==========] Running 32 tests from 7 test cases.
27: [----------] Global test environment set-up.
27: [----------] 4 tests from BasicAccessorPolicy
27: [ RUN ] BasicAccessorPolicy.Decay
27: [ OK ] BasicAccessorPolicy.Decay (0 ms)
27: [ RUN ] BasicAccessorPolicy.Access
27: [ OK ] BasicAccessorPolicy.Access (0 ms)
27: [ RUN ] BasicAccessorPolicy.Offset
27: [ OK ] BasicAccessorPolicy.Offset (0 ms)
27: [ RUN ] BasicAccessorPolicy.CopyAccessor
27: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms)
27: [----------] 4 tests from BasicAccessorPolicy (1 ms total)
27:
27: [----------] 4 tests from ExtentsTest
27: [ RUN ] ExtentsTest.Construction
27: [ OK ] ExtentsTest.Construction (0 ms)
27: [ RUN ] ExtentsTest.PurelyStatic
27: [ OK ] ExtentsTest.PurelyStatic (0 ms)
27: [ RUN ] ExtentsTest.RankNought
27: [ OK ] ExtentsTest.RankNought (0 ms)
27: [ RUN ] ExtentsTest.Assignment
27: [ OK ] ExtentsTest.Assignment (0 ms)
27: [----------] 4 tests from ExtentsTest (0 ms total)
27:
27: [----------] 8 tests from MdSpanExtension
27: [ RUN ] MdSpanExtension.SlicingAllStatic
27: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms)
27: [ RUN ] MdSpanExtension.SlicingDynamic
27: [ OK ] MdSpanExtension.SlicingDynamic (0 ms)
27: [ RUN ] MdSpanExtension.SlicingAllStatic3D
27: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms)
27: [ RUN ] MdSpanExtension.SlicingEqualsView3D
27: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms)
27: [ RUN ] MdSpanExtension.additionWorks
27: [ OK ] MdSpanExtension.additionWorks (0 ms)
27: [ RUN ] MdSpanExtension.subtractionWorks
27: [ OK ] MdSpanExtension.subtractionWorks (0 ms)
27: [ RUN ] MdSpanExtension.multiplicationWorks
27: [ OK ] MdSpanExtension.multiplicationWorks (0 ms)
27: [ RUN ] MdSpanExtension.divisionWorks
27: [ OK ] MdSpanExtension.divisionWorks (0 ms)
27: [----------] 8 tests from MdSpanExtension (0 ms total)
27:
27: [----------] 3 tests from LayoutTests
27: [ RUN ] LayoutTests.LayoutRightConstruction
27: [ OK ] LayoutTests.LayoutRightConstruction (0 ms)
27: [ RUN ] LayoutTests.LayoutRightProperties
27: [ OK ] LayoutTests.LayoutRightProperties (0 ms)
27: [ RUN ] LayoutTests.LayoutRightOperator
27: [ OK ] LayoutTests.LayoutRightOperator (0 ms)
27: [----------] 3 tests from LayoutTests (1 ms total)
27:
27: [----------] 1 test from MdSpanTest
27: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly
27: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms)
27: [----------] 1 test from MdSpanTest (0 ms total)
27:
27: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan<int, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<int> >
27: [ RUN ] MdSpanTest/0.Rank
27: [ OK ] MdSpanTest/0.Rank (0 ms)
27: [ RUN ] MdSpanTest/0.DynamicRank
27: [ OK ] MdSpanTest/0.DynamicRank (0 ms)
27: [ RUN ] MdSpanTest/0.Extents
27: [ OK ] MdSpanTest/0.Extents (0 ms)
27: [ RUN ] MdSpanTest/0.Strides
27: [ OK ] MdSpanTest/0.Strides (0 ms)
27: [ RUN ] MdSpanTest/0.Properties
27: [ OK ] MdSpanTest/0.Properties (0 ms)
27: [ RUN ] MdSpanTest/0.Operator
27: [ OK ] MdSpanTest/0.Operator (0 ms)
27: [----------] 6 tests from MdSpanTest/0 (0 ms total)
27:
27: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan<float, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<float> >
27: [ RUN ] MdSpanTest/1.Rank
27: [ OK ] MdSpanTest/1.Rank (0 ms)
27: [ RUN ] MdSpanTest/1.DynamicRank
27: [ OK ] MdSpanTest/1.DynamicRank (0 ms)
27: [ RUN ] MdSpanTest/1.Extents
27: [ OK ] MdSpanTest/1.Extents (0 ms)
27: [ RUN ] MdSpanTest/1.Strides
27: [ OK ] MdSpanTest/1.Strides (0 ms)
27: [ RUN ] MdSpanTest/1.Properties
27: [ OK ] MdSpanTest/1.Properties (0 ms)
27: [ RUN ] MdSpanTest/1.Operator
27: [ OK ] MdSpanTest/1.Operator (0 ms)
27: [----------] 6 tests from MdSpanTest/1 (0 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 32 tests from 7 test cases ran. (2 ms total)
27: [ PASSED ] 32 tests.
27/65 Test #27: MDSpanTests ........................... Passed 0.07 sec
test 28
Start 28: MdtypesUnitTest
28: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdtypes-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdtypesUnitTest.xml"
28: Test timeout computed to be: 30
28: [==========] Running 9 tests from 2 test cases.
28: [----------] Global test environment set-up.
28: [----------] 2 tests from CheckpointDataTest
28: [ RUN ] CheckpointDataTest.SingleDataTest
28: [ OK ] CheckpointDataTest.SingleDataTest (10 ms)
28: [ RUN ] CheckpointDataTest.MultiDataTest
28: [ OK ] CheckpointDataTest.MultiDataTest (60 ms)
28: [----------] 2 tests from CheckpointDataTest (70 ms total)
28:
28: [----------] 7 tests from ForceBuffers
28: [ RUN ] ForceBuffers.ConstructsUnpinned
28: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms)
28: [ RUN ] ForceBuffers.ConstructsPinned
28: [ OK ] ForceBuffers.ConstructsPinned (0 ms)
28: [ RUN ] ForceBuffers.ConstructsEmpty
28: [ OK ] ForceBuffers.ConstructsEmpty (0 ms)
28: [ RUN ] ForceBuffers.ResizeWorks
28: [ OK ] ForceBuffers.ResizeWorks (0 ms)
28: [ RUN ] ForceBuffers.PaddingWorks
28: [ OK ] ForceBuffers.PaddingWorks (0 ms)
28: [ RUN ] ForceBuffers.CopyWorks
28: [ OK ] ForceBuffers.CopyWorks (0 ms)
28: [ RUN ] ForceBuffers.CopyDoesNotPin
28: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms)
28: [----------] 7 tests from ForceBuffers (1 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 9 tests from 2 test cases ran. (71 ms total)
28: [ PASSED ] 9 tests.
28/65 Test #28: MdtypesUnitTest ....................... Passed 0.14 sec
test 29
Start 29: OnlineHelpUnitTests
29: Test command: /<<PKGBUILDDIR>>/build/basic/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml"
29: Test timeout computed to be: 30
29: [==========] Running 22 tests from 4 test cases.
29: [----------] Global test environment set-up.
29: [----------] 6 tests from TextTableFormatterTest
29: [ RUN ] TextTableFormatterTest.HandlesBasicCase
29: [ OK ] TextTableFormatterTest.HandlesBasicCase (55 ms)
29: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
29: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (11 ms)
29: [ RUN ] TextTableFormatterTest.HandlesIndentation
29: [ OK ] TextTableFormatterTest.HandlesIndentation (1 ms)
29: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
29: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (1 ms)
29: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
29: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (1 ms)
29: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
29: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (1 ms)
29: [----------] 6 tests from TextTableFormatterTest (70 ms total)
29:
29: [----------] 3 tests from HelpManagerTest
29: [ RUN ] HelpManagerTest.HandlesRootTopic
29: [ OK ] HelpManagerTest.HandlesRootTopic (1 ms)
29: [ RUN ] HelpManagerTest.HandlesSubTopics
29: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms)
29: [ RUN ] HelpManagerTest.HandlesInvalidTopics
29: [ OK ] HelpManagerTest.HandlesInvalidTopics (1 ms)
29: [----------] 3 tests from HelpManagerTest (2 ms total)
29:
29: [----------] 2 tests from HelpTopicFormattingTest
29: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
29: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (1 ms)
29: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
29: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms)
29: [----------] 2 tests from HelpTopicFormattingTest (2 ms total)
29:
29: [----------] 11 tests from HelpWriterContextTest
29: [ RUN ] HelpWriterContextTest.FormatsParagraphs
29: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
29: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (1 ms)
29: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
29: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsLiteralText
29: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
29: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
29: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsBulletList
29: [ OK ] HelpWriterContextTest.FormatsBulletList (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
29: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
29: [ OK ] HelpWriterContextTest.FormatsSimpleTable (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsGridTable
29: [ OK ] HelpWriterContextTest.FormatsGridTable (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsTitles
29: [ OK ] HelpWriterContextTest.FormatsTitles (1 ms)
29: [----------] 11 tests from HelpWriterContextTest (8 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 22 tests from 4 test cases ran. (82 ms total)
29: [ PASSED ] 22 tests.
29/65 Test #29: OnlineHelpUnitTests ................... Passed 0.15 sec
test 30
Start 30: OptionsUnitTests
30: Test command: /<<PKGBUILDDIR>>/build/basic/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OptionsUnitTests.xml"
30: Test timeout computed to be: 30
30: [==========] Running 111 tests from 18 test cases.
30: [----------] Global test environment set-up.
30: [----------] 5 tests from AbstractOptionStorageTest
30: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
30: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms)
30: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
30: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms)
30: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
30: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms)
30: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
30: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (1 ms)
30: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
30: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (1 ms)
30: [----------] 5 tests from AbstractOptionStorageTest (3 ms total)
30:
30: [----------] 10 tests from FileNameOptionTest
30: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
30: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
30: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
30: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
30: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
30: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
30: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
30: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
30: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms)
30: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
30: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension
30: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue
30: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms)
30: [----------] 10 tests from FileNameOptionTest (1 ms total)
30:
30: [----------] 15 tests from FileNameOptionManagerTest
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (1 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
30: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (1 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
30: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
30: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
30: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (1 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
30: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms)
30: [----------] 15 tests from FileNameOptionManagerTest (3 ms total)
30:
30: [----------] 1 test from OptionsTest
30: [ RUN ] OptionsTest.FailsOnNonsafeStorage
30: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms)
30: [----------] 1 test from OptionsTest (0 ms total)
30:
30: [----------] 9 tests from OptionsAssignerTest
30: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
30: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (1 ms)
30: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
30: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
30: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
30: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesMissingValue
30: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesExtraValue
30: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesGroups
30: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesSections
30: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
30: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
30: [----------] 9 tests from OptionsAssignerTest (2 ms total)
30:
30: [----------] 4 tests from OptionsAssignerBooleanTest
30: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
30: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms)
30: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
30: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
30: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
30: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
30: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
30: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms)
30: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total)
30:
30: [----------] 13 tests from OptionsAssignerIntegerTest
30: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
30: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (1 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
30: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
30: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
30: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
30: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
30: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
30: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
30: [----------] 13 tests from OptionsAssignerIntegerTest (2 ms total)
30:
30: [----------] 5 tests from OptionsAssignerDoubleTest
30: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
30: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
30: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
30: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
30: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
30: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
30: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total)
30:
30: [----------] 9 tests from OptionsAssignerStringTest
30: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
30: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
30: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
30: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
30: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
30: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
30: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
30: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
30: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
30: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
30: [----------] 9 tests from OptionsAssignerStringTest (0 ms total)
30:
30: [----------] 6 tests from OptionsAssignerEnumTest
30: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
30: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
30: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
30: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
30: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
30: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
30: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
30: [----------] 6 tests from OptionsAssignerEnumTest (1 ms total)
30:
30: [----------] 8 tests from RepeatingOptionSectionTest
30: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
30: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
30: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
30: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
30: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
30: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
30: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
30: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
30: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (1 ms)
30: [----------] 8 tests from RepeatingOptionSectionTest (1 ms total)
30:
30: [----------] 1 test from TimeUnitManagerTest
30: [ RUN ] TimeUnitManagerTest.BasicOperations
30: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
30: [----------] 1 test from TimeUnitManagerTest (0 ms total)
30:
30: [----------] 4 tests from TimeUnitBehaviorTest
30: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
30: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
30: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
30: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
30: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
30: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
30: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
30: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms)
30: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total)
30:
30: [----------] 2 tests from TreeValueSupportAssignTest
30: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
30: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms)
30: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
30: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
30: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total)
30:
30: [----------] 1 test from TreeValueSupportAssignErrorTest
30: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
30: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms)
30: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total)
30:
30: [----------] 5 tests from TreeValueSupportCheckTest
30: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
30: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
30: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
30: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
30: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
30: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
30: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total)
30:
30: [----------] 6 tests from TreeValueSupportAdjustTest
30: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
30: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (2 ms)
30: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
30: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
30: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (2 ms)
30: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
30: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
30: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (1 ms)
30: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
30: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms)
30: [----------] 6 tests from TreeValueSupportAdjustTest (5 ms total)
30:
30: [----------] 7 tests from TreeValueSupportTest
30: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
30: [ OK ] TreeValueSupportTest.SupportsBooleanOption (1 ms)
30: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
30: [ OK ] TreeValueSupportTest.SupportsIntegerOption (1 ms)
30: [ RUN ] TreeValueSupportTest.SupportsInt64Option
30: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms)
30: [ RUN ] TreeValueSupportTest.SupportsStringOption
30: [ OK ] TreeValueSupportTest.SupportsStringOption (1 ms)
30: [ RUN ] TreeValueSupportTest.SupportsFloatOption
30: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
30: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsEnumOption
30: [ OK ] TreeValueSupportTest.SupportsEnumOption (1 ms)
30: [----------] 7 tests from TreeValueSupportTest (6 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 111 tests from 18 test cases ran. (28 ms total)
30: [ PASSED ] 111 tests.
30/65 Test #30: OptionsUnitTests ...................... Passed 0.11 sec
test 31
Start 31: PbcutilUnitTest
31: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pbcutil-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/PbcutilUnitTest.xml"
31: Test timeout computed to be: 30
31: [==========] Running 33 tests from 5 test cases.
31: [----------] Global test environment set-up.
31: [----------] 1 test from ShiftTest
31: [ RUN ] ShiftTest.CoordinateShiftWorks
31: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms)
31: [----------] 1 test from ShiftTest (1 ms total)
31:
31: [----------] 2 tests from MShift
31: [ RUN ] MShift.shiftsAndUnshifts
31: [ OK ] MShift.shiftsAndUnshifts (1 ms)
31: [ RUN ] MShift.shiftsAndUnshiftsSelf
31: [ OK ] MShift.shiftsAndUnshiftsSelf (1 ms)
31: [----------] 2 tests from MShift (2 ms total)
31:
31: [----------] 1 test from PbcTest
31: [ RUN ] PbcTest.CalcShiftsWorks
31: [ OK ] PbcTest.CalcShiftsWorks (16 ms)
31: [----------] 1 test from PbcTest (17 ms total)
31:
31: [----------] 2 tests from PbcEnumsTest
31: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect
31: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms)
31: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect
31: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms)
31: [----------] 2 tests from PbcEnumsTest (1 ms total)
31:
31: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (16 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (16 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (3 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (3 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (3 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (3 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (4 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (1 ms)
31: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (99 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 33 tests from 5 test cases ran. (123 ms total)
31: [ PASSED ] 33 tests.
31/65 Test #31: PbcutilUnitTest ....................... Passed 0.20 sec
test 32
Start 32: RandomUnitTests
32: Test command: /<<PKGBUILDDIR>>/build/basic/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RandomUnitTests.xml"
32: Test timeout computed to be: 30
32: [==========] Running 44 tests from 10 test cases.
32: [----------] Global test environment set-up.
32: [----------] 4 tests from ExponentialDistributionTest
32: [ RUN ] ExponentialDistributionTest.Output
32: [ OK ] ExponentialDistributionTest.Output (11 ms)
32: [ RUN ] ExponentialDistributionTest.Logical
32: [ OK ] ExponentialDistributionTest.Logical (0 ms)
32: [ RUN ] ExponentialDistributionTest.Reset
32: [ OK ] ExponentialDistributionTest.Reset (0 ms)
32: [ RUN ] ExponentialDistributionTest.AltParam
32: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from ExponentialDistributionTest (12 ms total)
32:
32: [----------] 4 tests from GammaDistributionTest
32: [ RUN ] GammaDistributionTest.Output
32: [ OK ] GammaDistributionTest.Output (1 ms)
32: [ RUN ] GammaDistributionTest.Logical
32: [ OK ] GammaDistributionTest.Logical (0 ms)
32: [ RUN ] GammaDistributionTest.Reset
32: [ OK ] GammaDistributionTest.Reset (1 ms)
32: [ RUN ] GammaDistributionTest.AltParam
32: [ OK ] GammaDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from GammaDistributionTest (2 ms total)
32:
32: [----------] 4 tests from NormalDistributionTest
32: [ RUN ] NormalDistributionTest.Output
32: [ OK ] NormalDistributionTest.Output (1 ms)
32: [ RUN ] NormalDistributionTest.Logical
32: [ OK ] NormalDistributionTest.Logical (0 ms)
32: [ RUN ] NormalDistributionTest.Reset
32: [ OK ] NormalDistributionTest.Reset (0 ms)
32: [ RUN ] NormalDistributionTest.AltParam
32: [ OK ] NormalDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from NormalDistributionTest (2 ms total)
32:
32: [----------] 1 test from SeedTest
32: [ RUN ] SeedTest.makeRandomSeed
32: [ OK ] SeedTest.makeRandomSeed (1 ms)
32: [----------] 1 test from SeedTest (1 ms total)
32:
32: [----------] 6 tests from TabulatedNormalDistributionTest
32: [ RUN ] TabulatedNormalDistributionTest.Output14
32: [ OK ] TabulatedNormalDistributionTest.Output14 (2 ms)
32: [ RUN ] TabulatedNormalDistributionTest.Output16
32: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
32: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (1 ms)
32: [ RUN ] TabulatedNormalDistributionTest.Logical
32: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.Reset
32: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.AltParam
32: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
32: [----------] 6 tests from TabulatedNormalDistributionTest (4 ms total)
32:
32: [----------] 1 test from TabulatedNormalDistributionTableTest
32: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
32: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (8 ms)
32: [----------] 1 test from TabulatedNormalDistributionTableTest (8 ms total)
32:
32: [----------] 6 tests from ThreeFry2x64Test
32: [ RUN ] ThreeFry2x64Test.Logical
32: [ OK ] ThreeFry2x64Test.Logical (0 ms)
32: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
32: [ OK ] ThreeFry2x64Test.InternalCounterSequence (1 ms)
32: [ RUN ] ThreeFry2x64Test.Reseed
32: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
32: [ RUN ] ThreeFry2x64Test.Discard
32: [ OK ] ThreeFry2x64Test.Discard (0 ms)
32: [ RUN ] ThreeFry2x64Test.InvalidCounter
32: [ OK ] ThreeFry2x64Test.InvalidCounter (1 ms)
32: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
32: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
32: [----------] 6 tests from ThreeFry2x64Test (3 ms total)
32:
32: [----------] 4 tests from UniformIntDistributionTest
32: [ RUN ] UniformIntDistributionTest.Output
32: [ OK ] UniformIntDistributionTest.Output (1 ms)
32: [ RUN ] UniformIntDistributionTest.Logical
32: [ OK ] UniformIntDistributionTest.Logical (0 ms)
32: [ RUN ] UniformIntDistributionTest.Reset
32: [ OK ] UniformIntDistributionTest.Reset (0 ms)
32: [ RUN ] UniformIntDistributionTest.AltParam
32: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from UniformIntDistributionTest (2 ms total)
32:
32: [----------] 5 tests from UniformRealDistributionTest
32: [ RUN ] UniformRealDistributionTest.GenerateCanonical
32: [ OK ] UniformRealDistributionTest.GenerateCanonical (1 ms)
32: [ RUN ] UniformRealDistributionTest.Output
32: [ OK ] UniformRealDistributionTest.Output (1 ms)
32: [ RUN ] UniformRealDistributionTest.Logical
32: [ OK ] UniformRealDistributionTest.Logical (0 ms)
32: [ RUN ] UniformRealDistributionTest.Reset
32: [ OK ] UniformRealDistributionTest.Reset (0 ms)
32: [ RUN ] UniformRealDistributionTest.AltParam
32: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
32: [----------] 5 tests from UniformRealDistributionTest (2 ms total)
32:
32: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (1 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (1 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (1 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (1 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (1 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (1 ms)
32: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (7 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 44 tests from 10 test cases ran. (45 ms total)
32: [ PASSED ] 44 tests.
32/65 Test #32: RandomUnitTests ....................... Passed 0.15 sec
test 33
Start 33: RestraintTests
33: Test command: /<<PKGBUILDDIR>>/build/basic/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RestraintTests.xml"
33: Test timeout computed to be: 30
33: [==========] Running 1 test from 1 test case.
33: [----------] Global test environment set-up.
33: [----------] 1 test from RestraintManager
33: [ RUN ] RestraintManager.restraintList
33: [ OK ] RestraintManager.restraintList (0 ms)
33: [----------] 1 test from RestraintManager (0 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 1 test from 1 test case ran. (0 ms total)
33: [ PASSED ] 1 test.
33/65 Test #33: RestraintTests ........................ Passed 0.06 sec
test 34
Start 34: TableUnitTests
34: Test command: /<<PKGBUILDDIR>>/build/basic/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TableUnitTests.xml"
34: Test timeout computed to be: 30
34: [==========] Running 16 tests from 2 test cases.
34: [----------] Global test environment set-up.
34: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
34: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
34: [ OK ] SplineTableTest/0.HandlesIncorrectInput (8 ms)
34: [ RUN ] SplineTableTest/0.Sinc
34: [ OK ] SplineTableTest/0.Sinc (4 ms)
34: [ RUN ] SplineTableTest/0.LJ12
34: [ OK ] SplineTableTest/0.LJ12 (79 ms)
34: [ RUN ] SplineTableTest/0.PmeCorrection
34: [ OK ] SplineTableTest/0.PmeCorrection (8 ms)
34: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
34: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms)
34: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
34: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (6 ms)
34: [ RUN ] SplineTableTest/0.TwoFunctions
34: [ OK ] SplineTableTest/0.TwoFunctions (160 ms)
34: [ RUN ] SplineTableTest/0.ThreeFunctions
34: [ OK ] SplineTableTest/0.ThreeFunctions (188 ms)
34: [----------] 8 tests from SplineTableTest/0 (455 ms total)
34:
34: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
34: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
34: [ OK ] SplineTableTest/1.HandlesIncorrectInput (7 ms)
34: [ RUN ] SplineTableTest/1.Sinc
34: [ OK ] SplineTableTest/1.Sinc (4 ms)
34: [ RUN ] SplineTableTest/1.LJ12
34: [ OK ] SplineTableTest/1.LJ12 (12 ms)
34: [ RUN ] SplineTableTest/1.PmeCorrection
34: [ OK ] SplineTableTest/1.PmeCorrection (8 ms)
34: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
34: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms)
34: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
34: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (6 ms)
34: [ RUN ] SplineTableTest/1.TwoFunctions
34: [ OK ] SplineTableTest/1.TwoFunctions (24 ms)
34: [ RUN ] SplineTableTest/1.ThreeFunctions
34: [ OK ] SplineTableTest/1.ThreeFunctions (26 ms)
34: [----------] 8 tests from SplineTableTest/1 (88 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 16 tests from 2 test cases ran. (544 ms total)
34: [ PASSED ] 16 tests.
34/65 Test #34: TableUnitTests ........................ Passed 0.61 sec
test 35
Start 35: TaskAssignmentUnitTests
35: Test command: /<<PKGBUILDDIR>>/build/basic/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml"
35: Test timeout computed to be: 30
35: [==========] Running 3 tests from 2 test cases.
35: [----------] Global test environment set-up.
35: [----------] 2 tests from UserTaskAssignmentStringHandlingTest
35: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork
35: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (2 ms)
35: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid
35: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms)
35: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (3 ms total)
35:
35: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest
35: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow
35: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (2 ms)
35: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (2 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 3 tests from 2 test cases ran. (6 ms total)
35: [ PASSED ] 3 tests.
35/65 Test #35: TaskAssignmentUnitTests ............... Passed 0.07 sec
test 36
Start 36: TopologyTest
36: Test command: /<<PKGBUILDDIR>>/build/basic/bin/topology-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TopologyTest.xml"
36: Test timeout computed to be: 30
36: [==========] Running 31 tests from 5 test cases.
36: [----------] Global test environment set-up.
36: [----------] 3 tests from ExclusionBlockTest
36: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks
36: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms)
36: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka
36: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms)
36: [ RUN ] ExclusionBlockTest.MergeExclusions
36: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms)
36: [----------] 3 tests from ExclusionBlockTest (1 ms total)
36:
36: [----------] 6 tests from InteractionListTest
36: [ RUN ] InteractionListTest.EmptyWorks
36: [ OK ] InteractionListTest.EmptyWorks (0 ms)
36: [ RUN ] InteractionListTest.CanAddInteractionArray
36: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms)
36: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms
36: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms)
36: [ RUN ] InteractionListTest.CanAddInteractionPointer
36: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms)
36: [ RUN ] InteractionListTest.CanAddListToOtherList
36: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms)
36: [ RUN ] InteractionListTest.ClearingWorks
36: [ OK ] InteractionListTest.ClearingWorks (0 ms)
36: [----------] 6 tests from InteractionListTest (1 ms total)
36:
36: [----------] 3 tests from MtopTest
36: [ RUN ] MtopTest.RangeBasedLoop
36: [ OK ] MtopTest.RangeBasedLoop (0 ms)
36: [ RUN ] MtopTest.Operators
36: [ OK ] MtopTest.Operators (0 ms)
36: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms
36: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms)
36: [----------] 3 tests from MtopTest (0 ms total)
36:
36: [----------] 13 tests from StringTableTest
36: [ RUN ] StringTableTest.AddSingleEntry
36: [ OK ] StringTableTest.AddSingleEntry (4 ms)
36: [ RUN ] StringTableTest.CanAccessWithAt
36: [ OK ] StringTableTest.CanAccessWithAt (1 ms)
36: [ RUN ] StringTableTest.CanAccessWithBracket
36: [ OK ] StringTableTest.CanAccessWithBracket (2 ms)
36: [ RUN ] StringTableTest.ThrowsOutOfRange
36: [ OK ] StringTableTest.ThrowsOutOfRange (1 ms)
36: [ RUN ] StringTableTest.StringCompareIsCorrect
36: [ OK ] StringTableTest.StringCompareIsCorrect (2 ms)
36: [ RUN ] StringTableTest.AddTwoDistinctEntries
36: [ OK ] StringTableTest.AddTwoDistinctEntries (1 ms)
36: [ RUN ] StringTableTest.TryToAddDuplicates
36: [ OK ] StringTableTest.TryToAddDuplicates (1 ms)
36: [ RUN ] StringTableTest.AddLargeNumberOfEntries
36: [ OK ] StringTableTest.AddLargeNumberOfEntries (1 ms)
36: [ RUN ] StringTableTest.NoDuplicatesInLargeTable
36: [ OK ] StringTableTest.NoDuplicatesInLargeTable (1 ms)
36: [ RUN ] StringTableTest.CanWriteToBuffer
36: [ OK ] StringTableTest.CanWriteToBuffer (0 ms)
36: [ RUN ] StringTableTest.Roundtrip
36: [ OK ] StringTableTest.Roundtrip (1 ms)
36: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices
36: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms)
36: [ RUN ] StringTableTest.CanCopyToLegacyTable
36: [ OK ] StringTableTest.CanCopyToLegacyTable (1 ms)
36: [----------] 13 tests from StringTableTest (19 ms total)
36:
36: [----------] 6 tests from LegacySymtabTest
36: [ RUN ] LegacySymtabTest.EmptyOnOpen
36: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms)
36: [ RUN ] LegacySymtabTest.AddSingleEntry
36: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms)
36: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries
36: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms)
36: [ RUN ] LegacySymtabTest.TryToAddDuplicates
36: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms)
36: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries
36: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (2 ms)
36: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable
36: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms)
36: [----------] 6 tests from LegacySymtabTest (3 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 31 tests from 5 test cases ran. (24 ms total)
36: [ PASSED ] 31 tests.
36/65 Test #36: TopologyTest .......................... Passed 0.09 sec
test 37
Start 37: PullTest
37: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/PullTest.xml"
37: Test timeout computed to be: 30
37: [==========] Running 5 tests from 1 test case.
37: [----------] Global test environment set-up.
37: [----------] 5 tests from PullTest
37: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
37: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
37: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
37: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
37: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
37: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
37: [----------] 5 tests from PullTest (0 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 5 tests from 1 test case ran. (1 ms total)
37: [ PASSED ] 5 tests.
37/65 Test #37: PullTest .............................. Passed 0.06 sec
test 38
Start 38: SimdUnitTests
38: Test command: /<<PKGBUILDDIR>>/build/basic/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SimdUnitTests.xml"
38: Test timeout computed to be: 30
38: [==========] Running 86 tests from 3 test cases.
38: [----------] Global test environment set-up.
38: [----------] 41 tests from SimdScalarTest
38: [ RUN ] SimdScalarTest.load
38: [ OK ] SimdScalarTest.load (0 ms)
38: [ RUN ] SimdScalarTest.loadU
38: [ OK ] SimdScalarTest.loadU (0 ms)
38: [ RUN ] SimdScalarTest.store
38: [ OK ] SimdScalarTest.store (0 ms)
38: [ RUN ] SimdScalarTest.storeU
38: [ OK ] SimdScalarTest.storeU (0 ms)
38: [ RUN ] SimdScalarTest.setZero
38: [ OK ] SimdScalarTest.setZero (0 ms)
38: [ RUN ] SimdScalarTest.andNot
38: [ OK ] SimdScalarTest.andNot (0 ms)
38: [ RUN ] SimdScalarTest.fma
38: [ OK ] SimdScalarTest.fma (0 ms)
38: [ RUN ] SimdScalarTest.fms
38: [ OK ] SimdScalarTest.fms (0 ms)
38: [ RUN ] SimdScalarTest.fnma
38: [ OK ] SimdScalarTest.fnma (0 ms)
38: [ RUN ] SimdScalarTest.fnms
38: [ OK ] SimdScalarTest.fnms (0 ms)
38: [ RUN ] SimdScalarTest.maskAdd
38: [ OK ] SimdScalarTest.maskAdd (0 ms)
38: [ RUN ] SimdScalarTest.maskzMul
38: [ OK ] SimdScalarTest.maskzMul (0 ms)
38: [ RUN ] SimdScalarTest.maskzFma
38: [ OK ] SimdScalarTest.maskzFma (0 ms)
38: [ RUN ] SimdScalarTest.abs
38: [ OK ] SimdScalarTest.abs (0 ms)
38: [ RUN ] SimdScalarTest.max
38: [ OK ] SimdScalarTest.max (0 ms)
38: [ RUN ] SimdScalarTest.min
38: [ OK ] SimdScalarTest.min (0 ms)
38: [ RUN ] SimdScalarTest.round
38: [ OK ] SimdScalarTest.round (0 ms)
38: [ RUN ] SimdScalarTest.trunc
38: [ OK ] SimdScalarTest.trunc (0 ms)
38: [ RUN ] SimdScalarTest.reduce
38: [ OK ] SimdScalarTest.reduce (0 ms)
38: [ RUN ] SimdScalarTest.testBits
38: [ OK ] SimdScalarTest.testBits (0 ms)
38: [ RUN ] SimdScalarTest.anyTrue
38: [ OK ] SimdScalarTest.anyTrue (0 ms)
38: [ RUN ] SimdScalarTest.selectByMask
38: [ OK ] SimdScalarTest.selectByMask (0 ms)
38: [ RUN ] SimdScalarTest.selectByNotMask
38: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
38: [ RUN ] SimdScalarTest.blend
38: [ OK ] SimdScalarTest.blend (0 ms)
38: [ RUN ] SimdScalarTest.cvtR2I
38: [ OK ] SimdScalarTest.cvtR2I (0 ms)
38: [ RUN ] SimdScalarTest.cvttR2I
38: [ OK ] SimdScalarTest.cvttR2I (0 ms)
38: [ RUN ] SimdScalarTest.cvtI2R
38: [ OK ] SimdScalarTest.cvtI2R (0 ms)
38: [ RUN ] SimdScalarTest.cvtF2D
38: [ OK ] SimdScalarTest.cvtF2D (0 ms)
38: [ RUN ] SimdScalarTest.cvtD2D
38: [ OK ] SimdScalarTest.cvtD2D (0 ms)
38: [ RUN ] SimdScalarTest.loadI
38: [ OK ] SimdScalarTest.loadI (0 ms)
38: [ RUN ] SimdScalarTest.loadUI
38: [ OK ] SimdScalarTest.loadUI (0 ms)
38: [ RUN ] SimdScalarTest.storeI
38: [ OK ] SimdScalarTest.storeI (0 ms)
38: [ RUN ] SimdScalarTest.storeUI
38: [ OK ] SimdScalarTest.storeUI (0 ms)
38: [ RUN ] SimdScalarTest.andNotI
38: [ OK ] SimdScalarTest.andNotI (0 ms)
38: [ RUN ] SimdScalarTest.testBitsI
38: [ OK ] SimdScalarTest.testBitsI (0 ms)
38: [ RUN ] SimdScalarTest.selectByMaskI
38: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
38: [ RUN ] SimdScalarTest.selectByNotMaskI
38: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
38: [ RUN ] SimdScalarTest.blendI
38: [ OK ] SimdScalarTest.blendI (0 ms)
38: [ RUN ] SimdScalarTest.cvtB2IB
38: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
38: [ RUN ] SimdScalarTest.cvtIB2B
38: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
38: [ RUN ] SimdScalarTest.expandScalarsToTriplets
38: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
38: [----------] 41 tests from SimdScalarTest (3 ms total)
38:
38: [----------] 8 tests from SimdScalarUtilTest
38: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
38: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
38: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
38: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
38: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
38: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
38: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
38: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
38: [----------] 8 tests from SimdScalarUtilTest (0 ms total)
38:
38: [----------] 37 tests from SimdScalarMathTest
38: [ RUN ] SimdScalarMathTest.copysign
38: [ OK ] SimdScalarMathTest.copysign (0 ms)
38: [ RUN ] SimdScalarMathTest.invsqrtPair
38: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
38: [ RUN ] SimdScalarMathTest.inv
38: [ OK ] SimdScalarMathTest.inv (0 ms)
38: [ RUN ] SimdScalarMathTest.maskzInvsqrt
38: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
38: [ RUN ] SimdScalarMathTest.log
38: [ OK ] SimdScalarMathTest.log (0 ms)
38: [ RUN ] SimdScalarMathTest.exp2
38: [ OK ] SimdScalarMathTest.exp2 (0 ms)
38: [ RUN ] SimdScalarMathTest.exp
38: [ OK ] SimdScalarMathTest.exp (0 ms)
38: [ RUN ] SimdScalarMathTest.erf
38: [ OK ] SimdScalarMathTest.erf (0 ms)
38: [ RUN ] SimdScalarMathTest.erfc
38: [ OK ] SimdScalarMathTest.erfc (0 ms)
38: [ RUN ] SimdScalarMathTest.sincos
38: [ OK ] SimdScalarMathTest.sincos (0 ms)
38: [ RUN ] SimdScalarMathTest.sin
38: [ OK ] SimdScalarMathTest.sin (0 ms)
38: [ RUN ] SimdScalarMathTest.cos
38: [ OK ] SimdScalarMathTest.cos (0 ms)
38: [ RUN ] SimdScalarMathTest.tan
38: [ OK ] SimdScalarMathTest.tan (0 ms)
38: [ RUN ] SimdScalarMathTest.asin
38: [ OK ] SimdScalarMathTest.asin (0 ms)
38: [ RUN ] SimdScalarMathTest.acos
38: [ OK ] SimdScalarMathTest.acos (0 ms)
38: [ RUN ] SimdScalarMathTest.atan
38: [ OK ] SimdScalarMathTest.atan (0 ms)
38: [ RUN ] SimdScalarMathTest.atan2
38: [ OK ] SimdScalarMathTest.atan2 (0 ms)
38: [ RUN ] SimdScalarMathTest.pmeForceCorrection
38: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
38: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
38: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
38: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
38: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.invSingleAccuracy
38: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
38: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.logSingleAccuracy
38: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
38: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.expSingleAccuracy
38: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
38: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
38: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
38: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
38: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
38: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
38: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
38: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
38: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
38: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
38: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
38: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (1 ms)
38: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
38: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
38: [----------] 37 tests from SimdScalarMathTest (3 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 86 tests from 3 test cases ran. (6 ms total)
38: [ PASSED ] 86 tests.
38/65 Test #38: SimdUnitTests ......................... Passed 0.08 sec
test 39
Start 39: CompatibilityHelpersTests
39: Test command: /<<PKGBUILDDIR>>/build/basic/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml"
39: Test timeout computed to be: 30
39: [==========] Running 9 tests from 6 test cases.
39: [----------] Global test environment set-up.
39: [----------] 4 tests from TemplateMPTest
39: [ RUN ] TemplateMPTest.MpWithIndexInt
39: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms)
39: [ RUN ] TemplateMPTest.MpWithIndexIntBad
39: [ OK ] TemplateMPTest.MpWithIndexIntBad (1 ms)
39: [ RUN ] TemplateMPTest.MpWithIndexBool
39: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms)
39: [ RUN ] TemplateMPTest.MpWithIndexEnum
39: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms)
39: [----------] 4 tests from TemplateMPTest (1 ms total)
39:
39: [----------] 1 test from NotNullConstruction
39: [ RUN ] NotNullConstruction.Works
39: [ OK ] NotNullConstruction.Works (0 ms)
39: [----------] 1 test from NotNullConstruction (0 ms total)
39:
39: [----------] 1 test from NotNullCasting
39: [ RUN ] NotNullCasting.Works
39: [ OK ] NotNullCasting.Works (0 ms)
39: [----------] 1 test from NotNullCasting (0 ms total)
39:
39: [----------] 1 test from NotNullAssignment
39: [ RUN ] NotNullAssignment.Works
39: [ OK ] NotNullAssignment.Works (0 ms)
39: [----------] 1 test from NotNullAssignment (0 ms total)
39:
39: [----------] 1 test from MakeNotNull
39: [ RUN ] MakeNotNull.Works
39: [ OK ] MakeNotNull.Works (0 ms)
39: [----------] 1 test from MakeNotNull (1 ms total)
39:
39: [----------] 1 test from NotNull
39: [ RUN ] NotNull.WorksInContainers
39: [ OK ] NotNull.WorksInContainers (0 ms)
39: [----------] 1 test from NotNull (0 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 9 tests from 6 test cases ran. (5 ms total)
39: [ PASSED ] 9 tests.
39/65 Test #39: CompatibilityHelpersTests ............. Passed 0.07 sec
test 40
Start 40: GmxAnaTest
40: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxAnaTest.xml"
40: Test timeout computed to be: 600
40: [==========] Running 27 tests from 5 test cases.
40: [----------] Global test environment set-up.
40: [----------] 5 tests from Entropy
40: [ RUN ] Entropy.Schlitter_300_NoLinear
40: [ OK ] Entropy.Schlitter_300_NoLinear (39 ms)
40: [ RUN ] Entropy.Schlitter_300_Linear
40: [ OK ] Entropy.Schlitter_300_Linear (3 ms)
40: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
40: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (1 ms)
40: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
40: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (1 ms)
40: [ RUN ] Entropy.QuasiHarmonic_200_Linear
40: [ OK ] Entropy.QuasiHarmonic_200_Linear (1 ms)
40: [----------] 5 tests from Entropy (46 ms total)
40:
40: [----------] 10 tests from MindistTest
40: [ RUN ] MindistTest.mindistWorksWithSingleAtoms
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.mindistWorksWithSingleAtoms (17 ms)
40: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 2: 'atom3'
40: Selected 3: 'atoms12'
40: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (6 ms)
40: [ RUN ] MindistTest.mindistDoesNotPickUpContacts
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.mindistDoesNotPickUpContacts (6 ms)
40: [ RUN ] MindistTest.mindistPicksUpContacts
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.mindistPicksUpContacts (7 ms)
40: [ RUN ] MindistTest.ngWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: Selected 2: 'atom3'
40: [ OK ] MindistTest.ngWorks (6 ms)
40: [ RUN ] MindistTest.groupWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 3: 'atoms12'
40: Selected 2: 'atom3'
40: [ OK ] MindistTest.groupWorks (6 ms)
40: [ RUN ] MindistTest.maxDistWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 2: 'atom3'
40: Selected 3: 'atoms12'
40: [ OK ] MindistTest.maxDistWorks (6 ms)
40: [ RUN ] MindistTest.noPbcWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.noPbcWorks (6 ms)
40: [ RUN ] MindistTest.resPerTimeWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 3: 'atoms12'
40: Selected 2: 'atom3'
40: [ OK ] MindistTest.resPerTimeWorks (6 ms)
40: [ RUN ] MindistTest.matrixWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 5: 'atoms123'
40: Special case: making distance matrix between all atoms in group atoms123
40: [ OK ] MindistTest.matrixWorks (6 ms)
40: [----------] 10 tests from MindistTest (72 ms total)
40:
40: [----------] 3 tests from MsdTest
40: [ RUN ] MsdTest.threeDimensionalDiffusion
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( particles) has 3 elements
40: There is one group in the index
40:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
40:
40: Used 1 restart points spaced 200 ps over 9 ps
40:
40: Fitting from 1 to 8 ps
40:
40: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
40: [ OK ] MsdTest.threeDimensionalDiffusion (11 ms)
40: [ RUN ] MsdTest.twoDimensionalDiffusion
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( particles) has 3 elements
40: There is one group in the index
40:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
40:
40: Used 1 restart points spaced 200 ps over 9 ps
40:
40: Fitting from 1 to 8 ps
40:
40: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
40: [ OK ] MsdTest.twoDimensionalDiffusion (7 ms)
40: [ RUN ] MsdTest.oneDimensionalDiffusion
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( particles) has 3 elements
40: There is one group in the index
40:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
40:
40: Used 1 restart points spaced 200 ps over 9 ps
40:
40: Fitting from 1 to 8 ps
40:
40: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
40: [ OK ] MsdTest.oneDimensionalDiffusion (5 ms)
40: [----------] 3 tests from MsdTest (24 ms total)
40:
40: [----------] 3 tests from MsdMolTest
40: [ RUN ] MsdMolTest.diffMolMassWeighted
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Generating 1-4 interactions: fudge = 0.5
40: Number of degrees of freedom in T-Coupling group rest is 27.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Calculating diffusion coefficients for molecules.
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( water) has 15 elements
40: There is one group in the index
40: Split group of 15 atoms into 5 molecules
40: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
40:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
40:
40: Used 1 restart points spaced 200 ps over 0.1 ps
40:
40: Setting the LD random seed to -20332549
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40:
40: Generated 330891 of the 330891 1-4 parameter combinations
40:
40: Excluding 2 bonded neighbours molecule type 'SOL'
40:
40: This run will generate roughly 0 Mb of data
40: Wrote per-molecule output to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted_msdmol.xvg
40: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
40: Fitting from 0.008 to 0.088 ps
40:
40: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
40: [ OK ] MsdMolTest.diffMolMassWeighted (3339 ms)
40: [ RUN ] MsdMolTest.diffMolNonMassWeighted
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Generating 1-4 interactions: fudge = 0.5
40: Number of degrees of freedom in T-Coupling group rest is 27.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Calculating diffusion coefficients for molecules.
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( water) has 15 elements
40: There is one group in the index
40: Split group of 15 atoms into 5 molecules
40: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
40:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
40:
40: Used 1 restart points spaced 200 ps over 0.1 ps
40:
40: Setting the LD random seed to 2128328287
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40:
40: Generated 330891 of the 330891 1-4 parameter combinations
40:
40: Excluding 2 bonded neighbours molecule type 'SOL'
40:
40: This run will generate roughly 0 Mb of data
40: Wrote per-molecule output to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted_msdmol.xvg
40: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
40: Fitting from 0.008 to 0.088 ps
40:
40: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
40: [ OK ] MsdMolTest.diffMolNonMassWeighted (3364 ms)
40: [ RUN ] MsdMolTest.diffMolSelected
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Generating 1-4 interactions: fudge = 0.5
40: Number of degrees of freedom in T-Coupling group rest is 27.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Calculating diffusion coefficients for molecules.
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( mol) has 9 elements
40: There is one group in the index
40: Split group of 9 atoms into 3 molecules
40: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
40:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
40:
40: Used 1 restart points spaced 200 ps over 0.1 ps
40:
40: Setting the LD random seed to -1619158037
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40:
40: Generated 330891 of the 330891 1-4 parameter combinations
40:
40: Excluding 2 bonded neighbours molecule type 'SOL'
40:
40: This run will generate roughly 0 Mb of data
40: Wrote per-molecule output to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected_msdmol.xvg
40: <D> = 7.3593 Std. Dev. = 9.7910 Error = 5.6529
40: Fitting from 0.008 to 0.088 ps
40:
40: D[ mol] 7.8614 (+/- 1.5618) 1e-5 cm^2/s
40: [ OK ] MsdMolTest.diffMolSelected (3347 ms)
40: [----------] 3 tests from MsdMolTest (10053 ms total)
40:
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group: trr version: GMX_trn_file (single precision)
40:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (663 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (36 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (24 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group: Reading frames from gro file '', 6 atoms.
40:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (12 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
40:
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (42 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (9 ms)
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (787 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 27 tests from 5 test cases ran. (10984 ms total)
40: [ PASSED ] 27 tests.
40/65 Test #40: GmxAnaTest ............................ Passed 11.07 sec
test 41
Start 41: GmxPreprocessTests
41: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxPreprocessTests.xml"
41: Test timeout computed to be: 1920
41: [==========] Running 69 tests from 10 test cases.
41: [----------] Global test environment set-up.
41: [----------] 4 tests from GenconfTest
41: [ RUN ] GenconfTest.nbox_Works
41: [ OK ] GenconfTest.nbox_Works (41 ms)
41: [ RUN ] GenconfTest.nbox_norenumber_Works
41: [ OK ] GenconfTest.nbox_norenumber_Works (29 ms)
41: [ RUN ] GenconfTest.nbox_dist_Works
41: [ OK ] GenconfTest.nbox_dist_Works (22 ms)
41: [ RUN ] GenconfTest.nbox_rot_Works
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: [ OK ] GenconfTest.nbox_rot_Works (19 ms)
41: [----------] 4 tests from GenconfTest (111 ms total)
41:
41: [----------] 2 tests from GenionTest
41: [ RUN ] GenionTest.HighConcentrationIonPlacement
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
41: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
41: buffer. The cluster pair list does have a buffering effect, but choosing
41: a larger rlist might be necessary for good energy conservation.
41:
41:
41: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: Generating 1-4 interactions: fudge = 0.5
41: Number of degrees of freedom in T-Coupling group rest is 1308.00
41:
41: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
41: You are using a plain Coulomb cut-off, which might produce artifacts.
41: You might want to consider using PME electrostatics.
41:
41:
41:
41: There were 3 notes
41: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
41: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
41: Group 0 ( System) has 653 elements
41: Group 1 ( Water) has 648 elements
41: Group 2 ( SOL) has 648 elements
41: Group 3 ( non-Water) has 5 elements
41: Group 4 ( Other) has 5 elements
41: Group 5 ( METH) has 5 elements
41: Select a group: Number of (3-atomic) solvent molecules: 216
41: Using random seed 1997.
41: Replacing solvent molecule 56 (atom 168) with NA
41: Replacing solvent molecule 120 (atom 360) with NA
41: Replacing solvent molecule 182 (atom 546) with NA
41: Replacing solvent molecule 71 (atom 213) with NA
41: Replacing solvent molecule 189 (atom 567) with CL
41: Replacing solvent molecule 54 (atom 162) with CL
41: Replacing solvent molecule 155 (atom 465) with CL
41: Replacing solvent molecule 99 (atom 297) with CL
41:
41: Setting the LD random seed to -1343489025
41:
41: Generated 331705 of the 331705 non-bonded parameter combinations
41:
41: Generated 331705 of the 331705 1-4 parameter combinations
41:
41: Excluding 2 bonded neighbours molecule type 'SOL'
41:
41: Excluding 3 bonded neighbours molecule type 'methane'
41: Analysing residue names:
41: There are: 216 Water residues
41: There are: 1 Other residues
41: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
41:
41: This run will generate roughly 0 Mb of data
41: Will try to add 4 NA ions and 4 CL ions.
41: Select a continuous group of solvent molecules
41: Selected 1: 'Water'
41: [ OK ] GenionTest.HighConcentrationIonPlacement (3258 ms)
41: [ RUN ] GenionTest.NoIonPlacement
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
41: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
41: buffer. The cluster pair list does have a buffering effect, but choosing
41: a larger rlist might be necessary for good energy conservation.
41:
41:
41: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: Generating 1-4 interactions: fudge = 0.5
41: Number of degrees of freedom in T-Coupling group rest is 1308.00
41:
41: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
41: You are using a plain Coulomb cut-off, which might produce artifacts.
41: You might want to consider using PME electrostatics.
41:
41:
41:
41: There were 3 notes
41: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
41: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
41: No ions to add, will just copy input configuration.
41: Setting the LD random seed to -738201123
41:
41: Generated 331705 of the 331705 non-bonded parameter combinations
41:
41: Generated 331705 of the 331705 1-4 parameter combinations
41:
41: Excluding 2 bonded neighbours molecule type 'SOL'
41:
41: Excluding 3 bonded neighbours molecule type 'methane'
41: Analysing residue names:
41: There are: 216 Water residues
41: There are: 1 Other residues
41: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
41:
41: This run will generate roughly 0 Mb of data
41: [ OK ] GenionTest.NoIonPlacement (3156 ms)
41: [----------] 2 tests from GenionTest (6416 ms total)
41:
41: [----------] 1 test from GenRestrTest
41: [ RUN ] GenRestrTest.SimpleRestraintsGenerated
41:
41: Reading structure file
41: Group 0 ( System) has 156 elements
41: Group 1 ( Protein) has 156 elements
41: Group 2 ( Protein-H) has 75 elements
41: Group 3 ( C-alpha) has 10 elements
41: Group 4 ( Backbone) has 30 elements
41: Group 5 ( MainChain) has 40 elements
41: Group 6 ( MainChain+Cb) has 49 elements
41: Group 7 ( MainChain+H) has 52 elements
41: Group 8 ( SideChain) has 104 elements
41: Group 9 ( SideChain-H) has 35 elements
41: Select a group: Select group to position restrain
41: Selected 3: 'C-alpha'
41: [ OK ] GenRestrTest.SimpleRestraintsGenerated (59 ms)
41: [----------] 1 test from GenRestrTest (59 ms total)
41:
41: [----------] 9 tests from PreprocessingAtomTypesTest
41: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate
41: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid
41: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks
41: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks
41: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry
41: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound
41: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound
41: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber
41: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber
41: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms)
41: [----------] 9 tests from PreprocessingAtomTypesTest (3 ms total)
41:
41: [----------] 10 tests from PreprocessingBondAtomTypeTest
41: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate
41: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid
41: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks
41: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks
41: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry
41: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType
41: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound
41: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound
41: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber
41: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber
41: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms)
41: [----------] 10 tests from PreprocessingBondAtomTypeTest (3 ms total)
41:
41: [----------] 5 tests from InsertMoleculesTest
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
41: Reading solute configuration
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 8 atoms)!
41:
41: Added 1 molecules (out of 1 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
41:
41: Output configuration contains 8 atoms in 4 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (19 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 2 atoms)!
41:
Try 2 success (now 4 atoms)!
41:
Try 3 success (now 6 atoms)!
41:
Try 4 success (now 8 atoms)!
41:
Try 5 success (now 10 atoms)!
41:
41: Added 5 molecules (out of 5 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
41:
41: Output configuration contains 10 atoms in 10 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (11 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
41: Reading solute configuration
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 8 atoms)!
41:
Try 2 success (now 10 atoms)!
41:
41: Added 2 molecules (out of 2 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
41:
41: Output configuration contains 10 atoms in 4 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (12 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
41: Reading solute configuration
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 650 atoms)!
41:
Try 2 success (now 652 atoms)!
41:
Try 3 success (now 654 atoms)!
41:
Try 4 success (now 656 atoms)!
41:
41: Added 4 molecules (out of 4 requested)
41: Replaced 8 residues (24 atoms)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
41:
41: Output configuration contains 632 atoms in 212 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (89 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
41:
41:
Try 1 success (now 2 atoms)!
41:
Try 2 success (now 4 atoms)!
41:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
41:
Try 13 success (now 6 atoms)!
41:
41: Added 3 molecules (out of 4 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
41:
41: Output configuration contains 6 atoms in 3 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (33 ms)
41: [----------] 5 tests from InsertMoleculesTest (165 ms total)
41:
41: [----------] 14 tests from GetIrTest
41: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
41: Ignoring obsolete mdp entry 'title'
41: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (35 ms)
41: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals
41: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (28 ms)
41: [ RUN ] GetIrTest.AcceptsKeyWithoutValue
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsKeyWithoutValue (29 ms)
41: [ RUN ] GetIrTest.RejectsValueWithoutKey
41: [ OK ] GetIrTest.RejectsValueWithoutKey (28 ms)
41: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue
41: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (29 ms)
41: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (29 ms)
41: [ RUN ] GetIrTest.AcceptsEmptyLines
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsEmptyLines (23 ms)
41: [ RUN ] GetIrTest.AcceptsElectricField
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsElectricField (19 ms)
41: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (18 ms)
41: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (19 ms)
41: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys
41: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (11 ms)
41: [ RUN ] GetIrTest.AcceptsImplicitSolventNo
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsImplicitSolventNo (18 ms)
41: [ RUN ] GetIrTest.RejectsImplicitSolventYes
41: [ OK ] GetIrTest.RejectsImplicitSolventYes (28 ms)
41: [ RUN ] GetIrTest.AcceptsMimic
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsMimic (19 ms)
41: [----------] 14 tests from GetIrTest (333 ms total)
41:
41: [----------] 5 tests from SolvateTest
41: [ RUN ] SolvateTest.cs_box_Works
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 1x1x1 boxes
41: Solvent box contains 270 atoms in 90 residues
41: Removed 129 solvent atoms due to solvent-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 47 residues
41: Generated solvent containing 141 atoms in 47 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
41:
41: Output configuration contains 141 atoms in 47 residues
41: Volume : 1.331 (nm^3)
41: Density : 1056.36 (g/l)
41: Number of solvent molecules: 47
41:
41: [ OK ] SolvateTest.cs_box_Works (133 ms)
41: [ RUN ] SolvateTest.cs_cp_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 2x2x2 boxes
41: Solvent box contains 3660 atoms in 1220 residues
41: Removed 987 solvent atoms due to solvent-solvent overlap
41: Removed 15 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 886 residues
41: Generated solvent containing 2658 atoms in 886 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
41:
41: Output configuration contains 2664 atoms in 888 residues
41: Volume : 27.2709 (nm^3)
41: Density : 974.777 (g/l)
41: Number of solvent molecules: 886
41:
41: [ OK ] SolvateTest.cs_cp_Works (332 ms)
41: [ RUN ] SolvateTest.cs_cp_p_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 2x2x2 boxes
41: Solvent box contains 3660 atoms in 1220 residues
41: Removed 987 solvent atoms due to solvent-solvent overlap
41: Removed 15 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 886 residues
41: Generated solvent containing 2658 atoms in 886 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
41:
41: Output configuration contains 2664 atoms in 888 residues
41: Volume : 27.2709 (nm^3)
41: Density : 974.777 (g/l)
41: Number of solvent molecules: 886
41:
41: Processing topology
41: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top)
41: [ OK ] SolvateTest.cs_cp_p_Works (334 ms)
41: [ RUN ] SolvateTest.shell_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 2x2x2 boxes
41: Solvent box contains 3660 atoms in 1220 residues
41: Removed 987 solvent atoms due to solvent-solvent overlap
41: Removed 1902 solvent atoms more than 1.000000 nm from solute.
41: Removed 15 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 252 residues
41: Generated solvent containing 756 atoms in 252 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
41:
41: Output configuration contains 762 atoms in 254 residues
41: Volume : 27.2709 (nm^3)
41: Density : 279.3 (g/l)
41: Number of solvent molecules: 252
41:
41: [ OK ] SolvateTest.shell_Works (152 ms)
41: [ RUN ] SolvateTest.update_Topology_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 3x3x3 boxes
41: Solvent box contains 14952 atoms in 4984 residues
41: Removed 2787 solvent atoms due to solvent-solvent overlap
41: Removed 30 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 2 different molecule types:
41: HOH ( 3 atoms): 1876 residues
41: SOL ( 3 atoms): 2169 residues
41: Generated solvent containing 0 atoms in 0 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
41:
41: Output configuration contains 12141 atoms in 4047 residues
41: Volume : 125 (nm^3)
41: Density : 968.963 (g/l)
41: Number of solvent molecules: 4045
41:
41: Processing topology
41: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
41: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
41: [ OK ] SolvateTest.update_Topology_Works (1408 ms)
41: [----------] 5 tests from SolvateTest (2359 ms total)
41:
41: [----------] 1 test from TopDirTests
41: [ RUN ] TopDirTests.NamesArrayHasCorrectSize
41: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms)
41: [----------] 1 test from TopDirTests (0 ms total)
41:
41: [----------] 18 tests from SinglePeptideFragments/EditconfTest
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (128 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (36 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (41 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (51 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (16 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (17 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (25 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (29 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (18 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (55 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (35 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (34 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (18 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (14 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (15 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (18 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (13 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (14 ms)
41: [----------] 18 tests from SinglePeptideFragments/EditconfTest (580 ms total)
41:
41: [----------] Global test environment tear-down
41: [==========] 69 tests from 10 test cases ran. (10031 ms total)
41: [ PASSED ] 69 tests.
41/65 Test #41: GmxPreprocessTests .................... Passed 10.11 sec
test 42
Start 42: Pdb2gmx1Test
42: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx1Test.xml"
42: Test timeout computed to be: 1920
42: [==========] Running 24 tests from 1 test case.
42: [----------] Global test environment set-up.
42: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 0 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (688 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 0 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (764 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 0 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (620 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 0 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (565 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Marked 124 virtual sites
42: Added 16 dummy masses
42: Added 26 new constraints
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 130 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (665 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Marked 132 virtual sites
42: Added 10 dummy masses
42: Added 19 new constraints
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 133 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (694 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Marked 123 virtual sites
42: Added 22 dummy masses
42: Added 35 new constraints
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 132 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (651 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Marked 111 virtual sites
42: Added 18 dummy masses
42: Added 31 new constraints
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 116 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (642 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 0 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (626 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 0 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (741 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 0 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (620 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 0 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (632 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Marked 124 virtual sites
42: Added 16 dummy masses
42: Added 26 new constraints
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 130 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (628 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Marked 132 virtual sites
42: Added 10 dummy masses
42: Added 19 new constraints
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 133 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (795 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Marked 123 virtual sites
42: Added 22 dummy masses
42: Added 35 new constraints
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 132 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (674 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Marked 111 virtual sites
42: Added 18 dummy masses
42: Added 31 new constraints
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 116 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (668 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 0 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (589 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 0 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (755 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 0 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (612 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 0 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (645 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Marked 124 virtual sites
42: Added 16 dummy masses
42: Added 26 new constraints
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 130 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (637 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Marked 132 virtual sites
42: Added 10 dummy masses
42: Added 19 new constraints
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 133 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (788 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Marked 123 virtual sites
42: Added 22 dummy masses
42: Added 35 new constraints
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 132 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (651 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Marked 111 virtual sites
42: Added 18 dummy masses
42: Added 31 new constraints
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 116 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (684 ms)
42: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (16044 ms total)
42:
42: [----------] Global test environment tear-down
42: [==========] 24 tests from 1 test case ran. (16044 ms total)
42: [ PASSED ] 24 tests.
42/65 Test #42: Pdb2gmx1Test .......................... Passed 16.12 sec
test 43
Start 43: Pdb2gmx2Test
43: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx2Test.xml"
43: Test timeout computed to be: 1920
43: [==========] Running 32 tests from 2 test cases.
43: [----------] Global test environment set-up.
43: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (425 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (386 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (352 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (308 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 37 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 37 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (341 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 53 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 51 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (430 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 36 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 36 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (368 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 33 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 31 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (370 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (348 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (384 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (330 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (305 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 37 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 37 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (335 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 53 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 51 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (398 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 36 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 36 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (343 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 33 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 31 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (316 ms)
43: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (5748 ms total)
43:
43: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (399 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (430 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (368 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (372 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 39 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 39 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (385 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 57 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 55 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (444 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 38 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 38 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (389 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 35 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 33 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (409 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (367 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (431 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (363 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (344 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 39 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 39 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (402 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 57 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 55 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (649 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 38 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 38 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (390 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 35 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 33 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (356 ms)
43: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (6499 ms total)
43:
43: [----------] Global test environment tear-down
43: [==========] 32 tests from 2 test cases ran. (12248 ms total)
43: [ PASSED ] 32 tests.
43/65 Test #43: Pdb2gmx2Test .......................... Passed 12.32 sec
test 44
Start 44: Pdb2gmx3Test
44: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx3Test.xml"
44: Test timeout computed to be: 1920
44: [==========] Running 33 tests from 6 test cases.
44: [----------] Global test environment set-up.
44: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 653 pairs
44: Before cleaning: 691 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 255, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 691 dihedrals, 51 impropers, 457 angles
44: 650 pairs, 254 bonds and 0 virtual sites
44:
44: Total mass 1846.132 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (594 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 748 pairs
44: Before cleaning: 788 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 291, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 788 dihedrals, 72 impropers, 516 angles
44: 736 pairs, 290 bonds and 0 virtual sites
44:
44: Total mass 2088.366 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (631 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 676 pairs
44: Before cleaning: 727 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 262, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 727 dihedrals, 56 impropers, 472 angles
44: 667 pairs, 261 bonds and 0 virtual sites
44:
44: Total mass 1861.124 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (489 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 603 pairs
44: Before cleaning: 634 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 233, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 634 dihedrals, 48 impropers, 419 angles
44: 597 pairs, 232 bonds and 0 virtual sites
44:
44: Total mass 1662.888 a.m.u.
44:
44: Total charge -0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (538 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 124 virtual sites
44: Added 16 dummy masses
44: Added 26 new constraints
44: Before cleaning: 653 pairs
44: Before cleaning: 691 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 255, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 691 dihedrals, 51 impropers, 457 angles
44: 650 pairs, 254 bonds and 130 virtual sites
44:
44: Total mass 1846.132 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (525 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 132 virtual sites
44: Added 10 dummy masses
44: Added 19 new constraints
44: Before cleaning: 748 pairs
44: Before cleaning: 788 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 291, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 788 dihedrals, 72 impropers, 516 angles
44: 736 pairs, 290 bonds and 133 virtual sites
44:
44: Total mass 2088.366 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (632 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 123 virtual sites
44: Added 22 dummy masses
44: Added 35 new constraints
44: Before cleaning: 676 pairs
44: Before cleaning: 727 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 262, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 727 dihedrals, 56 impropers, 472 angles
44: 667 pairs, 261 bonds and 132 virtual sites
44:
44: Total mass 1861.124 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (589 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 111 virtual sites
44: Added 18 dummy masses
44: Added 31 new constraints
44: Before cleaning: 603 pairs
44: Before cleaning: 634 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 233, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 634 dihedrals, 48 impropers, 419 angles
44: 597 pairs, 232 bonds and 116 virtual sites
44:
44: Total mass 1662.888 a.m.u.
44:
44: Total charge -0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (481 ms)
44: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (4482 ms total)
44:
44: [----------] 1 test from ForAmber99sb_ildnWithTip4p/Pdb2gmxTest
44: [ RUN ] ForAmber99sb_ildnWithTip4p/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/tip4p.pdb...
44: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 2 4 (only water)
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (4 atoms, 2 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 2 residues with 8 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 4, now 4
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 2 angles
44: 0 pairs, 4 bonds and 0 virtual sites
44:
44: Total mass 36.032 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/tip4p.pdb.
44:
44: The Amber99sb-ildn force field and the tip4p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildnWithTip4p/Pdb2gmxTest.ProducesMatchingTopology/0 (146 ms)
44: [----------] 1 test from ForAmber99sb_ildnWithTip4p/Pdb2gmxTest (146 ms total)
44:
44: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 653 pairs
44: Before cleaning: 663 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 254, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 663 dihedrals, 48 impropers, 457 angles
44: 650 pairs, 254 bonds and 0 virtual sites
44:
44: Total mass 1846.115 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (532 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 748 pairs
44: Before cleaning: 778 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus PHE-33: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 290, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 778 dihedrals, 49 impropers, 516 angles
44: 736 pairs, 290 bonds and 0 virtual sites
44:
44: Total mass 2088.361 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (566 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 676 pairs
44: Before cleaning: 696 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44: Start terminus ALA-34: NH3+
44: End terminus ALA-49: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 261, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 696 dihedrals, 39 impropers, 472 angles
44: 667 pairs, 261 bonds and 0 virtual sites
44:
44: Total mass 1861.130 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (486 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 603 pairs
44: Before cleaning: 618 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44: Start terminus LYS-50: NH3+
44: End terminus PRO-65: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 232, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 618 dihedrals, 38 impropers, 419 angles
44: 597 pairs, 232 bonds and 0 virtual sites
44:
44: Total mass 1662.885 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (445 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 124 virtual sites
44: Added 16 dummy masses
44: Added 26 new constraints
44: Before cleaning: 653 pairs
44: Before cleaning: 663 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 254, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 663 dihedrals, 48 impropers, 457 angles
44: 650 pairs, 254 bonds and 130 virtual sites
44:
44: Total mass 1846.115 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (531 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 132 virtual sites
44: Added 10 dummy masses
44: Added 19 new constraints
44: Before cleaning: 748 pairs
44: Before cleaning: 778 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus PHE-33: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 290, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 778 dihedrals, 49 impropers, 516 angles
44: 736 pairs, 290 bonds and 133 virtual sites
44:
44: Total mass 2088.361 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (588 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 123 virtual sites
44: Added 22 dummy masses
44: Added 35 new constraints
44: Before cleaning: 676 pairs
44: Before cleaning: 696 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44: Start terminus ALA-34: NH3+
44: End terminus ALA-49: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 261, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 696 dihedrals, 39 impropers, 472 angles
44: 667 pairs, 261 bonds and 132 virtual sites
44:
44: Total mass 1861.130 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (536 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 111 virtual sites
44: Added 18 dummy masses
44: Added 31 new constraints
44: Before cleaning: 603 pairs
44: Before cleaning: 618 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44: Start terminus LYS-50: NH3+
44: End terminus PRO-65: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 232, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 618 dihedrals, 38 impropers, 419 angles
44: 597 pairs, 232 bonds and 116 virtual sites
44:
44: Total mass 1662.885 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (478 ms)
44: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (4166 ms total)
44:
44: [----------] 8 tests from ChainSep/Pdb2gmxTest
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 651 pairs
44: Before cleaning: 661 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on changing chain id only (ignoring TER records).
44:
44: Merged chains into joint molecule definitions at 2 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44: Start terminus PHE-6: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 258 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 258, now 258
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 10 cmap torsion pairs
44:
44: There are 661 dihedrals, 46 impropers, 463 angles
44: 648 pairs, 258 bonds and 0 virtual sites
44:
44: Total mass 1882.146 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (509 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 123 pairs
44: Before cleaning: 123 dihedrals
44: Keeping all generated dihedrals
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 10 donors and 7 acceptors were found.
44: There are 7 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS8
44: NE223
44: MET12 SD55 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 317 pairs
44: Before cleaning: 322 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on changing chain id only (ignoring TER records).
44:
44: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 4 28
44:
44: 2 'B' 7 58
44:
44: 3 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (28 atoms, 4 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 4 residues with 51 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 50, now 50
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 2 cmap torsion pairs
44:
44: There are 123 dihedrals, 9 impropers, 88 angles
44: 123 pairs, 50 bonds and 0 virtual sites
44:
44: Total mass 434.421 a.m.u.
44:
44: Total charge -2.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (58 atoms, 7 residues)
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus PHE-6: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 7 residues with 124 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 125, now 125
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 5 cmap torsion pairs
44:
44: There are 322 dihedrals, 19 impropers, 227 angles
44: 314 pairs, 125 bonds and 0 virtual sites
44:
44: Total mass 846.083 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 51 atoms 4 residues
44:
44: Including chain 2 in system: 124 atoms 7 residues
44:
44: Including chain 3 in system: 83 atoms 5 residues
44:
44: Now there are 258 atoms and 16 residues
44:
44: Total mass in system 1882.146 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (317 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 651 pairs
44: Before cleaning: 661 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records only (ignoring chain id).
44:
44: Merged chains into joint molecule definitions at 2 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ILE-9: COO-
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 258 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 258, now 258
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 10 cmap torsion pairs
44:
44: There are 661 dihedrals, 46 impropers, 463 angles
44: 648 pairs, 258 bonds and 0 virtual sites
44:
44: Total mass 1882.146 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (513 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 10 donors and 12 acceptors were found.
44: There are 13 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3
44: SG9
44: HIS8 NE251 1.055
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 288 pairs
44: Before cleaning: 293 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 152 pairs
44: Before cleaning: 152 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records only (ignoring chain id).
44:
44: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 8 61
44:
44: 2 'B' 3 25
44:
44: 3 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (61 atoms, 8 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ILE-9: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 8 residues with 114 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 115, now 115
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 6 cmap torsion pairs
44:
44: There are 293 dihedrals, 23 impropers, 203 angles
44: 285 pairs, 115 bonds and 0 virtual sites
44:
44: Total mass 888.952 a.m.u.
44:
44: Total charge -2.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (25 atoms, 3 residues)
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 61 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 60, now 60
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 152 dihedrals, 5 impropers, 112 angles
44: 152 pairs, 60 bonds and 0 virtual sites
44:
44: Total mass 391.552 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 114 atoms 8 residues
44:
44: Including chain 2 in system: 61 atoms 3 residues
44:
44: Including chain 3 in system: 83 atoms 5 residues
44:
44: Now there are 258 atoms and 16 residues
44:
44: Total mass in system 1882.146 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (390 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 650 pairs
44: Before cleaning: 660 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Merged chains into joint molecule definitions at 3 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44: Start terminus PHE-6: NH3+
44: End terminus ILE-9: COO-
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 261 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 260, now 260
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 8 cmap torsion pairs
44:
44: There are 660 dihedrals, 45 impropers, 466 angles
44: 647 pairs, 260 bonds and 0 virtual sites
44:
44: Total mass 1900.162 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (493 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 123 pairs
44: Before cleaning: 123 dihedrals
44: Keeping all generated dihedrals
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 6 donors and 4 acceptors were found.
44: There are 3 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 164 pairs
44: Before cleaning: 169 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 152 pairs
44: Before cleaning: 152 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 4 28
44:
44: 2 'B' 4 33
44:
44: 3 'B' 3 25
44:
44: 4 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (28 atoms, 4 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 4 residues with 51 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 50, now 50
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 2 cmap torsion pairs
44:
44: There are 123 dihedrals, 9 impropers, 88 angles
44: 123 pairs, 50 bonds and 0 virtual sites
44:
44: Total mass 434.421 a.m.u.
44:
44: Total charge -2.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (33 atoms, 4 residues)
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44: Start terminus PHE-6: NH3+
44: End terminus ILE-9: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 4 residues with 66 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 67, now 67
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 2 cmap torsion pairs
44:
44: There are 169 dihedrals, 13 impropers, 118 angles
44: 161 pairs, 67 bonds and 0 virtual sites
44:
44: Total mass 472.547 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'B' (25 atoms, 3 residues)
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 61 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 60, now 60
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 152 dihedrals, 5 impropers, 112 angles
44: 152 pairs, 60 bonds and 0 virtual sites
44:
44: Total mass 391.552 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Processing chain 4 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 51 atoms 4 residues
44:
44: Including chain 2 in system: 66 atoms 4 residues
44:
44: Including chain 3 in system: 61 atoms 3 residues
44:
44: Including chain 4 in system: 83 atoms 5 residues
44:
44: Now there are 261 atoms and 16 residues
44:
44: Total mass in system 1900.162 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (311 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 652 pairs
44: Before cleaning: 662 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records and chain id changing.
44:
44: Merged chains into joint molecule definitions at 1 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 256, now 256
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 12 cmap torsion pairs
44:
44: There are 662 dihedrals, 47 impropers, 460 angles
44: 649 pairs, 256 bonds and 0 virtual sites
44:
44: Total mass 1864.131 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (615 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 14 donors and 15 acceptors were found.
44: There are 20 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 441 pairs
44: Before cleaning: 446 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records and chain id changing.
44:
44: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 11 86
44:
44: 2 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (86 atoms, 11 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 11 residues with 172 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 173, now 173
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 9 cmap torsion pairs
44:
44: There are 446 dihedrals, 29 impropers, 312 angles
44: 438 pairs, 173 bonds and 0 virtual sites
44:
44: Total mass 1262.488 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 172 atoms 11 residues
44:
44: Including chain 2 in system: 83 atoms 5 residues
44:
44: Now there are 255 atoms and 16 residues
44:
44: Total mass in system 1864.131 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (342 ms)
44: [----------] 8 tests from ChainSep/Pdb2gmxTest (3492 ms total)
44:
44: [----------] 4 tests from ChainChanges/Pdb2gmxTest
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on changing chain id only (ignoring TER records).
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge -0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (228 ms)
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records only (ignoring chain id).
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge -0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (233 ms)
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge -0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (296 ms)
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records and chain id changing.
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge -0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (233 ms)
44: [----------] 4 tests from ChainChanges/Pdb2gmxTest (995 ms total)
44:
44: [----------] 4 tests from ForCharmm27CyclicSystem/Pdb2gmxTest
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: WARNING: all CONECT records are ignored
44: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 6040 pairs
44: Before cleaning: 6605 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 6040 pairs
44: Before cleaning: 6605 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb...
44: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: Moved all the water blocks to the end
44:
44: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms
44:
44: chain #res #atoms
44:
44: 1 'P' 71 1527
44:
44: 2 'Q' 71 1527
44:
44: 3 'Q' 7 7
44:
44: 4 ' ' 10 10 (only water)
44:
44: 5 ' ' 16 16 (only water)
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'P' (1527 atoms, 71 residues)
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 71 residues with 2297 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 2481, now 2481
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 6605 dihedrals, 183 impropers, 4434 angles
44: 5827 pairs, 2481 bonds and 0 virtual sites
44:
44: Total mass 22984.514 a.m.u.
44:
44: Total charge -71.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'Q' (1527 atoms, 71 residues)
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 71 residues with 2297 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 2481, now 2481
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 6605 dihedrals, 183 impropers, 4434 angles
44: 5827 pairs, 2481 bonds and 0 virtual sites
44:
44: Total mass 22984.514 a.m.u.
44:
44: Total charge -71.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'Q' (7 atoms, 7 residues)
44:
44: Residue MG72 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG73 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG74 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG75 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG76 has type 'Ion', assuming it is not linked into a chain.
44:
44: Disabling further notes about ions.
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 7 residues with 7 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: No bonds
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 0 angles
44: 0 pairs, 0 bonds and 0 virtual sites
44:
44: Total mass 170.135 a.m.u.
44:
44: Total charge 14.000 e
44:
44: Writing topology
44:
44: Processing chain 4 (10 atoms, 10 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 10 residues with 30 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 30, now 30
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 30 angles
44: 0 pairs, 30 bonds and 0 virtual sites
44:
44: Total mass 180.154 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Processing chain 5 (16 atoms, 16 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 48 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 48, now 48
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 48 angles
44: 0 pairs, 48 bonds and 0 virtual sites
44:
44: Total mass 288.246 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Including chain 1 in system: 2297 atoms 71 residues
44:
44: Including chain 2 in system: 2297 atoms 71 residues
44:
44: Including chain 3 in system: 7 atoms 7 residues
44:
44: Including chain 4 in system: 30 atoms 10 residues
44:
44: Including chain 5 in system: 48 atoms 16 residues
44:
44: Now there are 4679 atoms and 175 residues
44:
44: Total mass in system 46607.562 a.m.u.
44:
44: Total charge in system -128.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/0 (46531 ms)
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 2325 pairs
44: Before cleaning: 2325 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb...
44: Read 'CARNOCYCLIN-A', 413 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 60 413
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (413 atoms, 60 residues)
44:
44: Identified residue LEU1 as a starting terminus.
44:
44: Identified residue LEU60 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 60 residues with 878 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 880, now 880
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 59 cmap torsion pairs
44:
44: There are 2325 dihedrals, 137 impropers, 1614 angles
44: 2319 pairs, 880 bonds and 0 virtual sites
44:
44: Total mass 5866.087 a.m.u.
44:
44: Total charge 4.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/1 (3619 ms)
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: WARNING: all CONECT records are ignored
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 12080 pairs
44: Before cleaning: 13210 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb...
44: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Moved all the water blocks to the end
44:
44: Merged chains into joint molecule definitions at 2 places.
44:
44: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms
44:
44: chain #res #atoms
44:
44: 1 'P' 149 3061
44:
44: 2 ' ' 10 10 (only water)
44:
44: 3 ' ' 16 16 (only water)
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'P' (3061 atoms, 149 residues)
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Residue MG72 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG73 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG74 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG75 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG76 has type 'Ion', assuming it is not linked into a chain.
44:
44: Disabling further notes about ions.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 149 residues with 4601 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 4962, now 4962
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 13210 dihedrals, 366 impropers, 8868 angles
44: 11654 pairs, 4962 bonds and 0 virtual sites
44:
44: Total mass 46139.162 a.m.u.
44:
44: Total charge -128.000 e
44:
44: Writing topology
44:
44: Processing chain 2 (10 atoms, 10 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 10 residues with 30 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 30, now 30
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 30 angles
44: 0 pairs, 30 bonds and 0 virtual sites
44:
44: Total mass 180.154 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Processing chain 3 (16 atoms, 16 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 48 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 48, now 48
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 48 angles
44: 0 pairs, 48 bonds and 0 virtual sites
44:
44: Total mass 288.246 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Including chain 1 in system: 4601 atoms 149 residues
44:
44: Including chain 2 in system: 30 atoms 10 residues
44:
44: Including chain 3 in system: 48 atoms 16 residues
44:
44: Now there are 4679 atoms and 175 residues
44:
44: Total mass in system 46607.562 a.m.u.
44:
44: Total charge in system -128.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/2 (105728 ms)
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 2325 pairs
44: Before cleaning: 2325 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb...
44: Read 'CARNOCYCLIN-A', 413 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 60 413
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (413 atoms, 60 residues)
44:
44: Identified residue LEU1 as a starting terminus.
44:
44: Identified residue LEU60 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 60 residues with 878 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 880, now 880
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 59 cmap torsion pairs
44:
44: There are 2325 dihedrals, 137 impropers, 1614 angles
44: 2319 pairs, 880 bonds and 0 virtual sites
44:
44: Total mass 5866.087 a.m.u.
44:
44: Total charge 4.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/3 (3331 ms)
44: [----------] 4 tests from ForCharmm27CyclicSystem/Pdb2gmxTest (159213 ms total)
44:
44: [----------] Global test environment tear-down
44: [==========] 33 tests from 6 test cases ran. (172496 ms total)
44: [ PASSED ] 33 tests.
44/65 Test #44: Pdb2gmx3Test .......................... Passed 172.57 sec
test 45
Start 45: CorrelationsTest
45: Test command: /<<PKGBUILDDIR>>/build/basic/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CorrelationsTest.xml"
45: Test timeout computed to be: 30
45: [==========] Running 21 tests from 3 test cases.
45: [----------] Global test environment set-up.
45: [----------] 10 tests from AutocorrTest
45: [ RUN ] AutocorrTest.EacNormal
45: [ OK ] AutocorrTest.EacNormal (39 ms)
45: [ RUN ] AutocorrTest.EacNoNormalize
45: [ OK ] AutocorrTest.EacNoNormalize (22 ms)
45: [ RUN ] AutocorrTest.EacCos
45: [ OK ] AutocorrTest.EacCos (31 ms)
45: [ RUN ] AutocorrTest.EacVector
45: [ OK ] AutocorrTest.EacVector (42 ms)
45: [ RUN ] AutocorrTest.EacRcross
45: [ OK ] AutocorrTest.EacRcross (9 ms)
45: [ RUN ] AutocorrTest.EacP0
45: [ OK ] AutocorrTest.EacP0 (43 ms)
45: [ RUN ] AutocorrTest.EacP1
45: [ OK ] AutocorrTest.EacP1 (42 ms)
45: [ RUN ] AutocorrTest.EacP2
45: [ OK ] AutocorrTest.EacP2 (79 ms)
45: [ RUN ] AutocorrTest.EacP3
45: [ OK ] AutocorrTest.EacP3 (24 ms)
45: [ RUN ] AutocorrTest.EacP4
45: [ OK ] AutocorrTest.EacP4 (42 ms)
45: [----------] 10 tests from AutocorrTest (382 ms total)
45:
45: [----------] 10 tests from ExpfitTest
45: [ RUN ] ExpfitTest.EffnEXP1
45: [ OK ] ExpfitTest.EffnEXP1 (4 ms)
45: [ RUN ] ExpfitTest.EffnEXP2
45: [ OK ] ExpfitTest.EffnEXP2 (7 ms)
45: [ RUN ] ExpfitTest.EffnEXPEXP
45: [ OK ] ExpfitTest.EffnEXPEXP (12 ms)
45: [ RUN ] ExpfitTest.EffnEXP5
45: [ OK ] ExpfitTest.EffnEXP5 (36 ms)
45: [ RUN ] ExpfitTest.EffnEXP7
45: [ OK ] ExpfitTest.EffnEXP7 (30 ms)
45: [ RUN ] ExpfitTest.EffnEXP9
45: [ OK ] ExpfitTest.EffnEXP9 (230 ms)
45: [ RUN ] ExpfitTest.EffnERF
45: [ OK ] ExpfitTest.EffnERF (19 ms)
45: [ RUN ] ExpfitTest.EffnERREST
45: [ OK ] ExpfitTest.EffnERREST (21 ms)
45: [ RUN ] ExpfitTest.EffnVAC
45: [ OK ] ExpfitTest.EffnVAC (40 ms)
45: [ RUN ] ExpfitTest.EffnPRES
45: [ OK ] ExpfitTest.EffnPRES (101 ms)
45: [----------] 10 tests from ExpfitTest (502 ms total)
45:
45: [----------] 1 test from ManyAutocorrelationTest
45: [ RUN ] ManyAutocorrelationTest.Empty
45: [ OK ] ManyAutocorrelationTest.Empty (0 ms)
45: [----------] 1 test from ManyAutocorrelationTest (0 ms total)
45:
45: [----------] Global test environment tear-down
45: [==========] 21 tests from 3 test cases ran. (952 ms total)
45: [ PASSED ] 21 tests.
45/65 Test #45: CorrelationsTest ...................... Passed 1.02 sec
test 46
Start 46: AnalysisDataUnitTests
46: Test command: /<<PKGBUILDDIR>>/build/basic/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml"
46: Test timeout computed to be: 30
46: [==========] Running 69 tests from 14 test cases.
46: [----------] Global test environment set-up.
46: [----------] 3 tests from AnalysisDataInitializationTest
46: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
46: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms)
46: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
46: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (2 ms)
46: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
46: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms)
46: [----------] 3 tests from AnalysisDataInitializationTest (2 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
46: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (2 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (4 ms)
46: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (2 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (1 ms)
46: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (1 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/0 (24 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
46: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (5 ms)
46: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (2 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (1 ms)
46: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (1 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/1 (26 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
46: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (5 ms)
46: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (2 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (2 ms)
46: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (2 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/2 (32 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
46: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (5 ms)
46: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (2 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (2 ms)
46: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (3 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/3 (30 ms total)
46:
46: [----------] 4 tests from AnalysisArrayDataTest
46: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
46: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (4 ms)
46: [ RUN ] AnalysisArrayDataTest.StorageWorks
46: [ OK ] AnalysisArrayDataTest.StorageWorks (2 ms)
46: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
46: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms)
46: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
46: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
46: [----------] 4 tests from AnalysisArrayDataTest (7 ms total)
46:
46: [----------] 6 tests from AverageModuleTest
46: [ RUN ] AverageModuleTest.BasicTest
46: [ OK ] AverageModuleTest.BasicTest (32 ms)
46: [ RUN ] AverageModuleTest.HandlesMultipointData
46: [ OK ] AverageModuleTest.HandlesMultipointData (20 ms)
46: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
46: [ OK ] AverageModuleTest.HandlesMultipleDataSets (6 ms)
46: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
46: [ OK ] AverageModuleTest.HandlesDataSetAveraging (6 ms)
46: [ RUN ] AverageModuleTest.CanCustomizeXAxis
46: [ OK ] AverageModuleTest.CanCustomizeXAxis (4 ms)
46: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
46: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (4 ms)
46: [----------] 6 tests from AverageModuleTest (77 ms total)
46:
46: [----------] 2 tests from FrameAverageModuleTest
46: [ RUN ] FrameAverageModuleTest.BasicTest
46: [ OK ] FrameAverageModuleTest.BasicTest (5 ms)
46: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
46: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (6 ms)
46: [----------] 2 tests from FrameAverageModuleTest (13 ms total)
46:
46: [----------] 7 tests from AnalysisHistogramSettingsTest
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
46: [----------] 7 tests from AnalysisHistogramSettingsTest (4 ms total)
46:
46: [----------] 2 tests from SimpleHistogramModuleTest
46: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
46: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (7 ms)
46: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
46: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (7 ms)
46: [----------] 2 tests from SimpleHistogramModuleTest (16 ms total)
46:
46: [----------] 3 tests from WeightedHistogramModuleTest
46: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
46: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (7 ms)
46: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
46: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (8 ms)
46: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
46: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (8 ms)
46: [----------] 3 tests from WeightedHistogramModuleTest (25 ms total)
46:
46: [----------] 3 tests from BinAverageModuleTest
46: [ RUN ] BinAverageModuleTest.ComputesCorrectly
46: [ OK ] BinAverageModuleTest.ComputesCorrectly (6 ms)
46: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
46: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (6 ms)
46: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
46: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (6 ms)
46: [----------] 3 tests from BinAverageModuleTest (20 ms total)
46:
46: [----------] 4 tests from AbstractAverageHistogramTest
46: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
46: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (8 ms)
46: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
46: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (8 ms)
46: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
46: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (7 ms)
46: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
46: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (6 ms)
46: [----------] 4 tests from AbstractAverageHistogramTest (31 ms total)
46:
46: [----------] 3 tests from LifetimeModuleTest
46: [ RUN ] LifetimeModuleTest.BasicTest
46: [ OK ] LifetimeModuleTest.BasicTest (5 ms)
46: [ RUN ] LifetimeModuleTest.CumulativeTest
46: [ OK ] LifetimeModuleTest.CumulativeTest (4 ms)
46: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
46: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (5 ms)
46: [----------] 3 tests from LifetimeModuleTest (17 ms total)
46:
46: [----------] Global test environment tear-down
46: [==========] 69 tests from 14 test cases ran. (330 ms total)
46: [ PASSED ] 69 tests.
46/65 Test #46: AnalysisDataUnitTests ................. Passed 0.41 sec
test 47
Start 47: CoordinateIOTests
47: Test command: /<<PKGBUILDDIR>>/build/basic/bin/coordinateio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CoordinateIOTests.xml"
47: Test timeout computed to be: 30
47: [==========] Running 64 tests from 19 test cases.
47: [----------] Global test environment set-up.
47: [----------] 1 test from OutputSelectorDeathTest
47: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (38 ms)
47: [----------] 1 test from OutputSelectorDeathTest (39 ms total)
47:
47: [----------] 5 tests from TrajectoryFrameWriterTest
47: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (27 ms)
47: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (27 ms)
47: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (27 ms)
47: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (52 ms)
47: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks
47: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms)
47: [----------] 5 tests from TrajectoryFrameWriterTest (134 ms total)
47:
47: [----------] 5 tests from OutputAdapterContainer
47: [ RUN ] OutputAdapterContainer.MakeEmpty
47: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms)
47: [ RUN ] OutputAdapterContainer.AddAdapter
47: [ OK ] OutputAdapterContainer.AddAdapter (0 ms)
47: [ RUN ] OutputAdapterContainer.RejectBadAdapter
47: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms)
47: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter
47: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms)
47: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters
47: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms)
47: [----------] 5 tests from OutputAdapterContainer (1 ms total)
47:
47: [----------] 5 tests from FlagTest
47: [ RUN ] FlagTest.CanSetSimpleFlag
47: [ OK ] FlagTest.CanSetSimpleFlag (0 ms)
47: [ RUN ] FlagTest.CanAddNewBox
47: [ OK ] FlagTest.CanAddNewBox (1 ms)
47: [ RUN ] FlagTest.SetsImplicitPrecisionChange
47: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms)
47: [ RUN ] FlagTest.SetsImplicitStartTimeChange
47: [ OK ] FlagTest.SetsImplicitStartTimeChange (1 ms)
47: [ RUN ] FlagTest.SetsImplicitTimeStepChange
47: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms)
47: [----------] 5 tests from FlagTest (3 ms total)
47:
47: [----------] 5 tests from SetAtomsTest
47: [ RUN ] SetAtomsTest.RemovesExistingAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.RemovesExistingAtoms (27 ms)
47: [ RUN ] SetAtomsTest.AddsNewAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.AddsNewAtoms (26 ms)
47: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (26 ms)
47: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (26 ms)
47: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (27 ms)
47: [----------] 5 tests from SetAtomsTest (134 ms total)
47:
47: [----------] 2 tests from SetBothTimeTest
47: [ RUN ] SetBothTimeTest.StartTimeZeroWorks
47: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms)
47: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks
47: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms)
47: [----------] 2 tests from SetBothTimeTest (1 ms total)
47:
47: [----------] 2 tests from SetStartTimeTest
47: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart
47: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms)
47: [ RUN ] SetStartTimeTest.WorksWithZeroStart
47: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms)
47: [----------] 2 tests from SetStartTimeTest (1 ms total)
47:
47: [----------] 1 test from SetTimeStepTest
47: [ RUN ] SetTimeStepTest.SetTimeStepWorks
47: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms)
47: [----------] 1 test from SetTimeStepTest (1 ms total)
47:
47: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (26 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (26 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (26 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (26 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (26 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (26 ms)
47: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (160 ms total)
47:
47: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles
47: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (26 ms)
47: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (26 ms)
47: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (26 ms)
47: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (80 ms total)
47:
47: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (1 ms)
47: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms)
47: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (1 ms total)
47:
47: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (53 ms)
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (54 ms)
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (54 ms)
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (54 ms)
47: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (219 ms total)
47:
47: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles
47: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (27 ms)
47: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (26 ms)
47: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (26 ms)
47: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (81 ms total)
47:
47: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms)
47: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (1 ms total)
47:
47: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles
47: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (26 ms)
47: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (26 ms)
47: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (53 ms total)
47:
47: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms)
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms)
47: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (1 ms total)
47:
47: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles
47: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (26 ms)
47: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (26 ms)
47: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (53 ms total)
47:
47: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms)
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms)
47: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (2 ms total)
47:
47: [----------] 4 tests from ModuleSupported/NoOptionalOutput
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (26 ms)
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (26 ms)
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (26 ms)
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (27 ms)
47: [----------] 4 tests from ModuleSupported/NoOptionalOutput (107 ms total)
47:
47: [----------] Global test environment tear-down
47: [==========] 64 tests from 19 test cases ran. (1079 ms total)
47: [ PASSED ] 64 tests.
47/65 Test #47: CoordinateIOTests ..................... Passed 1.16 sec
test 48
Start 48: TrajectoryAnalysisUnitTests
48: Test command: /<<PKGBUILDDIR>>/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
48: Test timeout computed to be: 1920
48: [==========] Running 82 tests from 16 test cases.
48: [----------] Global test environment set-up.
48: [----------] 11 tests from AngleModuleTest
48: [ RUN ] AngleModuleTest.ComputesSimpleAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesSimpleAngles (72 ms)
48: [ RUN ] AngleModuleTest.ComputesDihedrals
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesDihedrals (20 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorPairAngles (34 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (20 ms)
48: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (19 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (19 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
48: Reading frames from gro file 'Test system for different angles', 33 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (23 ms)
48: [ RUN ] AngleModuleTest.ComputesMultipleAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesMultipleAngles (21 ms)
48: [ RUN ] AngleModuleTest.HandlesDynamicSelections
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.HandlesDynamicSelections (19 ms)
48: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (19 ms)
48: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (20 ms)
48: [----------] 11 tests from AngleModuleTest (294 ms total)
48:
48: [----------] 5 tests from ClustsizeTest
48: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
48: There is one group in the index
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 24
48: cmid: 2, cmax: 4, max_size: 6
48: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
48: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (27 ms)
48: [ RUN ] ClustsizeTest.NoMolShortCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
48: There is one group in the index
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 24
48: cmid: 1, cmax: 6, max_size: 6
48: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
48: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (14 ms)
48: [ RUN ] ClustsizeTest.MolDefaultCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 8
48: cmid: 2, cmax: 4, max_size: 2
48: 50%100%cmid: 2, cmax: 6, max_size: 2
48: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (32 ms)
48: [ RUN ] ClustsizeTest.MolShortCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 8
48: cmid: 1, cmax: 6, max_size: 2
48: 50%100%cmid: 2, cmax: 6, max_size: 2
48: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (15 ms)
48: [ RUN ] ClustsizeTest.MolCSize
48: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 8
48: cmid: 2, cmax: 4, max_size: 2
48: 50%100%cmid: 2, cmax: 6, max_size: 2
48: 50%100%[ OK ] ClustsizeTest.MolCSize (16 ms)
48: [----------] 5 tests from ClustsizeTest (105 ms total)
48:
48: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (4 ms)
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
48: Reading frames from gro file 'Test system', 8 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (18 ms)
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
48: Reading frames from gro file 'Test system', 8 atoms.
48:
Reading frame 0 time 0.000
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (18 ms)
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (2 ms)
48: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (44 ms total)
48:
48: [----------] 4 tests from ConvertTrjModuleTest
48: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (62 ms)
48: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (55 ms)
48: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (11 ms)
48: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (11 ms)
48: [----------] 4 tests from ConvertTrjModuleTest (140 ms total)
48:
48: [----------] 3 tests from DistanceModuleTest
48: [ RUN ] DistanceModuleTest.ComputesDistances
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: atomname S1 S2:
48: Number of samples: 5
48: Average distance: 1.43246 nm
48: Standard deviation: 0.96700 nm
48: [ OK ] DistanceModuleTest.ComputesDistances (24 ms)
48: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: atomname S1 S2:
48: Number of samples: 5
48: Average distance: 1.43246 nm
48: Standard deviation: 0.96700 nm
48: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
48: Number of samples: 4
48: Average distance: 1.81066 nm
48: Standard deviation: 0.79289 nm
48: [ OK ] DistanceModuleTest.ComputesMultipleDistances (26 ms)
48: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: atomname S1 S2 and res_cog x < 2.8:
48: Number of samples: 3
48: Average distance: 1.72076 nm
48: Standard deviation: 1.24839 nm
48: [ OK ] DistanceModuleTest.HandlesDynamicSelections (25 ms)
48: [----------] 3 tests from DistanceModuleTest (78 ms total)
48:
48: [----------] 2 tests from ExtractClusterModuleTest
48: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms
48: trr version: GMX_trn_file (single precision)
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
48: Analyzed 26 frames, last time 0.050
48: There are 8 clusters containing 26 structures, highest framenr is 25
48: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (20 ms)
48: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
48: Analyzed 26 frames, last time 0.050
48: There are 8 clusters containing 26 structures, highest framenr is 25
48: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (16 ms)
48: [----------] 2 tests from ExtractClusterModuleTest (38 ms total)
48:
48: [----------] 2 tests from FreeVolumeModuleTest
48: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for 40 particles. These were set to zero.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: cutoff = 0.18 nm
48: probe_radius = 0 nm
48: seed = 13
48: ninsert = 1000 probes per nm^3
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
48: van der Spoel and Luciano T. Costa
48: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
48: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
48: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
48: -------- -------- --- Thank You --- -------- --------
48:
48: Free volume 38.02 +/- 0.00 %
48: Total volume 68.92 +/- 0.00 nm^3
48: Number of molecules 340 total mass 63491.38 Dalton
48: Average molar mass: 186.74 Dalton
48: Density rho: 1529.71 +/- 0.00 nm^3
48: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
48: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
48: Fractional free volume 0.194 +/- 0.000
48: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (766 ms)
48: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: cutoff = 0.18 nm
48: probe_radius = 0 nm
48: seed = 17
48: ninsert = 1000 probes per nm^3
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
48: van der Spoel and Luciano T. Costa
48: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
48: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
48: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
48: -------- -------- --- Thank You --- -------- --------
48:
48: Free volume 38.48 +/- 0.00 %
48: Total volume 68.92 +/- 0.00 nm^3
48: Number of molecules 340 total mass 63491.38 Dalton
48: Average molar mass: 186.74 Dalton
48: Density rho: 1529.71 +/- 0.00 nm^3
48: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
48: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
48: Fractional free volume 0.200 +/- 0.000
48: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (662 ms)
48: [----------] 2 tests from FreeVolumeModuleTest (1428 ms total)
48:
48: [----------] 9 tests from PairDistanceModuleTest
48: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesAllDistances (27 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (19 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (19 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (21 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (19 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (19 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (19 ms)
48: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (19 ms)
48: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (19 ms)
48: [----------] 9 tests from PairDistanceModuleTest (183 ms total)
48:
48: [----------] 5 tests from RdfModuleTest
48: [ RUN ] RdfModuleTest.BasicTest
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.BasicTest (172 ms)
48: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
48: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (225 ms)
48: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (164 ms)
48: [ RUN ] RdfModuleTest.CalculatesSurf
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.CalculatesSurf (108 ms)
48: [ RUN ] RdfModuleTest.CalculatesXY
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.CalculatesXY (179 ms)
48: [----------] 5 tests from RdfModuleTest (855 ms total)
48:
48: [----------] 5 tests from SasaModuleTest
48: [ RUN ] SasaModuleTest.BasicTest
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.BasicTest (83 ms)
48: [ RUN ] SasaModuleTest.HandlesSelectedResidues
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.HandlesSelectedResidues (53 ms)
48: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (46 ms)
48: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (62 ms)
48: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (61 ms)
48: [----------] 5 tests from SasaModuleTest (317 ms total)
48:
48: [----------] 8 tests from SelectModuleTest
48: [ RUN ] SelectModuleTest.BasicTest
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.BasicTest (34 ms)
48: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (26 ms)
48: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (26 ms)
48: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (26 ms)
48: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (26 ms)
48: [ RUN ] SelectModuleTest.NormalizesSizes
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.NormalizesSizes (19 ms)
48: [ RUN ] SelectModuleTest.WritesResidueNumbers
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.WritesResidueNumbers (19 ms)
48: [ RUN ] SelectModuleTest.WritesResidueIndices
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.WritesResidueIndices (18 ms)
48: [----------] 8 tests from SelectModuleTest (197 ms total)
48:
48: [----------] 10 tests from SurfaceAreaTest
48: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
48: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms)
48: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
48: [ OK ] SurfaceAreaTest.ComputesTwoPoints (6 ms)
48: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
48: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (6 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints12
48: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints32
48: [ OK ] SurfaceAreaTest.SurfacePoints32 (3 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints42
48: [ OK ] SurfaceAreaTest.SurfacePoints42 (3 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints122
48: [ OK ] SurfaceAreaTest.SurfacePoints122 (9 ms)
48: [ RUN ] SurfaceAreaTest.Computes100Points
48: [ OK ] SurfaceAreaTest.Computes100Points (4 ms)
48: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
48: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (14 ms)
48: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
48: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (16 ms)
48: [----------] 10 tests from SurfaceAreaTest (65 ms total)
48:
48: [----------] 4 tests from TopologyInformation
48: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
48: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms)
48: [ RUN ] TopologyInformation.WorksWithGroFile
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TopologyInformation.WorksWithGroFile (28 ms)
48: [ RUN ] TopologyInformation.WorksWithPdbFile
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TopologyInformation.WorksWithPdbFile (27 ms)
48: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Generating 1-4 interactions: fudge = 0.5
48:
48: NOTE 2 [file lysozyme.top, line 1465]:
48: System has non-zero total charge: 2.000000
48: Total charge should normally be an integer. See
48: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
48: for discussion on how close it should be to an integer.
48:
48:
48:
48: Number of degrees of freedom in T-Coupling group rest is 465.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
48: Setting the LD random seed to 2147294710
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48:
48: Generated 330891 of the 330891 1-4 parameter combinations
48:
48: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
48: Analysing residue names:
48: There are: 10 Protein residues
48: Analysing Protein...
48:
48: This run will generate roughly 0 Mb of data
48: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (3519 ms)
48: [----------] 4 tests from TopologyInformation (3574 ms total)
48:
48: [----------] 4 tests from TrajectoryModuleTest
48: [ RUN ] TrajectoryModuleTest.BasicTest
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.BasicTest (22 ms)
48: [ RUN ] TrajectoryModuleTest.PlotsXOnly
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.PlotsXOnly (22 ms)
48: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (20 ms)
48: [ RUN ] TrajectoryModuleTest.HandlesNoForces
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.HandlesNoForces (19 ms)
48: [----------] 4 tests from TrajectoryModuleTest (85 ms total)
48:
48: [----------] 5 tests from UnionFinderTest
48: [ RUN ] UnionFinderTest.WorksEmpty
48: [ OK ] UnionFinderTest.WorksEmpty (0 ms)
48: [ RUN ] UnionFinderTest.BasicMerges
48: [ OK ] UnionFinderTest.BasicMerges (0 ms)
48: [ RUN ] UnionFinderTest.LargerMerges
48: [ OK ] UnionFinderTest.LargerMerges (0 ms)
48: [ RUN ] UnionFinderTest.LongRightMerge
48: [ OK ] UnionFinderTest.LongRightMerge (0 ms)
48: [ RUN ] UnionFinderTest.LongLeftMerge
48: [ OK ] UnionFinderTest.LongLeftMerge (0 ms)
48: [----------] 5 tests from UnionFinderTest (0 ms total)
48:
48: [----------] 1 test from MappedUnionFinderTest
48: [ RUN ] MappedUnionFinderTest.BasicMerges
48: [ OK ] MappedUnionFinderTest.BasicMerges (1 ms)
48: [----------] 1 test from MappedUnionFinderTest (1 ms total)
48:
48: [----------] Global test environment tear-down
48: [==========] 82 tests from 16 test cases ran. (7406 ms total)
48: [ PASSED ] 82 tests.
48/65 Test #48: TrajectoryAnalysisUnitTests ........... Passed 7.49 sec
test 49
Start 49: EnergyAnalysisUnitTests
49: Test command: /<<PKGBUILDDIR>>/build/basic/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml"
49: Test timeout computed to be: 30
49: [==========] Running 7 tests from 4 test cases.
49: [----------] Global test environment set-up.
49: [----------] 1 test from DhdlTest
49: [ RUN ] DhdlTest.ExtractDhdl
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
49: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
49: Note: file tpx version 110, software tpx version 122
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
49:
49:
49: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
49: [ OK ] DhdlTest.ExtractDhdl (147 ms)
49: [----------] 1 test from DhdlTest (150 ms total)
49:
49: [----------] 1 test from OriresTest
49: [ RUN ] OriresTest.ExtractOrires
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
49: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
49: Note: file tpx version 111, software tpx version 122
49: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
49: End your selection with 0
49: Selecting all 7 orientation restraints
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
49: [ OK ] OriresTest.ExtractOrires (86 ms)
49: [----------] 1 test from OriresTest (87 ms total)
49:
49: [----------] 3 tests from EnergyTest
49: [ RUN ] EnergyTest.ExtractEnergy
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
49: Select the terms you want from the following list by
49: selecting either (part of) the name or the number or a combination.
49: End your selection with an empty line or a zero.
49: -------------------------------------------------------------------
49: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
49: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
49: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
49: 13 Box-Z 14 Volume 15 Density 16 pV
49: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
49: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
49: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
49: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
49: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
49: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
49:
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
49: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
49: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
49: [ OK ] EnergyTest.ExtractEnergy (24 ms)
49: [ RUN ] EnergyTest.ExtractEnergyByNumber
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
49: Select the terms you want from the following list by
49: selecting either (part of) the name or the number or a combination.
49: End your selection with an empty line or a zero.
49: -------------------------------------------------------------------
49: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
49: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
49: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
49: 13 Box-Z 14 Volume 15 Density 16 pV
49: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
49: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
49: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
49: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
49: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
49: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
49:
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
49: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
49: Pres. DC -268.49 3 8.52175 13.2804 (bar)
49: [ OK ] EnergyTest.ExtractEnergyByNumber (22 ms)
49: [ RUN ] EnergyTest.ExtractEnergyMixed
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
49: Select the terms you want from the following list by
49: selecting either (part of) the name or the number or a combination.
49: End your selection with an empty line or a zero.
49: -------------------------------------------------------------------
49: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
49: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
49: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
49: 13 Box-Z 14 Volume 15 Density 16 pV
49: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
49: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
49: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
49: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
49: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
49: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
49:
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
49: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
49: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
49: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
49: [ OK ] EnergyTest.ExtractEnergyMixed (23 ms)
49: [----------] 3 tests from EnergyTest (75 ms total)
49:
49: [----------] 2 tests from ViscosityTest
49: [ RUN ] ViscosityTest.EinsteinViscosity
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Pres-XX 20.2092 65 717.193 185.978 (bar)
49: Pres-XY -47.7351 39 372.522 207.456 (bar)
49: Pres-XZ 11.477 31 379.79 6.80818 (bar)
49: Pres-YX -47.7106 39 372.525 207.5 (bar)
49: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
49: Pres-YZ -41.3534 45 401.216 114.663 (bar)
49: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
49: Pres-ZY -41.3119 45 401.196 114.743 (bar)
49: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
49: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
49: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
49: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
49: [ OK ] ViscosityTest.EinsteinViscosity (47 ms)
49: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Pres-XX 20.2092 65 717.193 185.978 (bar)
49: Pres-XY -47.7351 39 372.522 207.456 (bar)
49: Pres-XZ 11.477 31 379.79 6.80818 (bar)
49: Pres-YX -47.7106 39 372.525 207.5 (bar)
49: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
49: Pres-YZ -41.3534 45 401.216 114.663 (bar)
49: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
49: Pres-ZY -41.3119 45 401.196 114.743 (bar)
49: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
49: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
49: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
49: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
49: [ OK ] ViscosityTest.EinsteinViscosityIntegral (61 ms)
49: [----------] 2 tests from ViscosityTest (110 ms total)
49:
49: [----------] Global test environment tear-down
49: [==========] 7 tests from 4 test cases ran. (423 ms total)
49: [ PASSED ] 7 tests.
49/65 Test #49: EnergyAnalysisUnitTests ............... Passed 0.49 sec
test 50
Start 50: ToolUnitTests
50: Test command: /<<PKGBUILDDIR>>/build/basic/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/ToolUnitTests.xml"
50: Test timeout computed to be: 1920
50: [==========] Running 21 tests from 5 test cases.
50: [----------] Global test environment set-up.
50: [----------] 2 tests from DumpTest
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
50: For a correct single-point energy evaluation with nsteps = 0, use
50: continuation = yes to avoid constraining the input coordinates.
50:
50: Generating 1-4 interactions: fudge = 0.5
50:
50: NOTE 2 [file lysozyme.top, line 1465]:
50: System has non-zero total charge: 2.000000
50: Total charge should normally be an integer. See
50: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
50: for discussion on how close it should be to an integer.
50:
50:
50:
50: Number of degrees of freedom in T-Coupling group rest is 465.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
50: NVE simulation with an initial temperature of zero: will use a Verlet
50: buffer of 10%. Check your energy drift!
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Setting the LD random seed to -17564197
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50:
50: Generated 330891 of the 330891 1-4 parameter combinations
50:
50: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
50: Analysing residue names:
50: There are: 10 Protein residues
50: Analysing Protein...
50:
50: This run will generate roughly 0 Mb of data
50: [ RUN ] DumpTest.WorksWithTpr
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
50: /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr:
50: inputrec:
50: integrator = md
50: tinit = 0
50: dt = 0.001
50: nsteps = 0
50: init-step = 0
50: simulation-part = 1
50: mts = false
50: comm-mode = Linear
50: nstcomm = 100
50: bd-fric = 0
50: ld-seed = -17564197
50: emtol = 10
50: emstep = 0.01
50: niter = 20
50: fcstep = 0
50: nstcgsteep = 1000
50: nbfgscorr = 10
50: rtpi = 0.05
50: nstxout = 0
50: nstvout = 0
50: nstfout = 0
50: nstlog = 1000
50: nstcalcenergy = 100
50: nstenergy = 1000
50: nstxout-compressed = 0
50: compressed-x-precision = 1000
50: cutoff-scheme = Verlet
50: nstlist = 10
50: pbc = xyz
50: periodic-molecules = false
50: verlet-buffer-tolerance = -1
50: rlist = 1.1
50: coulombtype = Cut-off
50: coulomb-modifier = Potential-shift
50: rcoulomb-switch = 0
50: rcoulomb = 1
50: epsilon-r = 1
50: epsilon-rf = inf
50: vdw-type = Cut-off
50: vdw-modifier = Potential-shift
50: rvdw-switch = 0
50: rvdw = 1
50: DispCorr = No
50: table-extension = 1
50: fourierspacing = 0.12
50: fourier-nx = 0
50: fourier-ny = 0
50: fourier-nz = 0
50: pme-order = 4
50: ewald-rtol = 1e-05
50: ewald-rtol-lj = 0.001
50: lj-pme-comb-rule = Geometric
50: ewald-geometry = 0
50: epsilon-surface = 0
50: tcoupl = No
50: nsttcouple = -1
50: nh-chain-length = 0
50: print-nose-hoover-chain-variables = false
50: pcoupl = No
50: pcoupltype = Isotropic
50: nstpcouple = -1
50: tau-p = 1
50: compressibility (3x3):
50: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: ref-p (3x3):
50: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: refcoord-scaling = No
50: posres-com (3):
50: posres-com[0]= 0.00000e+00
50: posres-com[1]= 0.00000e+00
50: posres-com[2]= 0.00000e+00
50: posres-comB (3):
50: posres-comB[0]= 0.00000e+00
50: posres-comB[1]= 0.00000e+00
50: posres-comB[2]= 0.00000e+00
50: QMMM = false
50: qm-opts:
50: ngQM = 0
50: constraint-algorithm = Lincs
50: continuation = false
50: Shake-SOR = false
50: shake-tol = 0.0001
50: lincs-order = 4
50: lincs-iter = 1
50: lincs-warnangle = 30
50: nwall = 0
50: wall-type = 9-3
50: wall-r-linpot = -1
50: wall-atomtype[0] = -1
50: wall-atomtype[1] = -1
50: wall-density[0] = 0
50: wall-density[1] = 0
50: wall-ewald-zfac = 3
50: pull = false
50: awh = false
50: rotation = false
50: interactiveMD = false
50: disre = No
50: disre-weighting = Conservative
50: disre-mixed = false
50: dr-fc = 1000
50: dr-tau = 0
50: nstdisreout = 100
50: orire-fc = 0
50: orire-tau = 0
50: nstorireout = 100
50: free-energy = no
50: cos-acceleration = 0
50: deform (3x3):
50: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: simulated-tempering = false
50: swapcoords = no
50: userint1 = 0
50: userint2 = 0
50: userint3 = 0
50: userint4 = 0
50: userreal1 = 0
50: userreal2 = 0
50: userreal3 = 0
50: userreal4 = 0
50: applied-forces:
50: electric-field:
50: x:
50: E0 = 0
50: omega = 0
50: t0 = 0
50: sigma = 0
50: y:
50: E0 = 0
50: omega = 0
50: t0 = 0
50: sigma = 0
50: z:
50: E0 = 0
50: omega = 0
50: t0 = 0
50: sigma = 0
50: density-guided-simulation:
50: active = false
50: group = protein
50: similarity-measure = inner-product
50: atom-spreading-weight = unity
50: force-constant = 1e+09
50: gaussian-transform-spreading-width = 0.2
50: gaussian-transform-spreading-range-in-multiples-of-width = 4
50: reference-density-filename = reference.mrc
50: nst = 1
50: normalize-densities = true
50: adaptive-force-scaling = false
50: adaptive-force-scaling-time-constant = 4
50: shift-vector =
50: transformation-matrix =
50: grpopts:
50: nrdf: 465
50: ref-t: 0
50: tau-t: 0
50: annealing: No
50: annealing-npoints: 0
50: acc: 0 0 0
50: nfreeze: N N N
50: energygrp-flags[ 0]: 0
50: header:
50: bIr = present
50: bBox = present
50: bTop = present
50: bX = present
50: bV = present
50: bF = not present
50: natoms = 156
50: lambda = 0.000000e+00
50: buffer size = 59458
50: topology:
50: name="First 10 residues from 1AKI"
50: #atoms = 156
50: #molblock = 1
50: molblock (0):
50: moltype = 0 "Protein_chain_B"
50: #molecules = 1
50: #posres_xA = 0
50: #posres_xB = 0
50: bIntermolecularInteractions = false
50: ffparams:
50: atnr=10
50: ntypes=212
50: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06
50: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06
50: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07
50: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06
50: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06
50: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06
50: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07
50: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07
50: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05
50: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06
50: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06
50: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07
50: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06
50: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06
50: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06
50: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07
50: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07
50: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05
50: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07
50: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07
50: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08
50: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07
50: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07
50: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07
50: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08
50: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08
50: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06
50: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06
50: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06
50: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07
50: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05
50: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06
50: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06
50: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07
50: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07
50: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05
50: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06
50: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06
50: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07
50: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06
50: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06
50: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06
50: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07
50: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07
50: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06
50: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06
50: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06
50: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07
50: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06
50: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06
50: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06
50: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07
50: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07
50: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05
50: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07
50: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07
50: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08
50: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07
50: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07
50: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07
50: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08
50: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08
50: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07
50: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07
50: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07
50: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08
50: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07
50: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07
50: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07
50: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08
50: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08
50: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07
50: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05
50: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05
50: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06
50: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05
50: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06
50: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05
50: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07
50: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07
50: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05
50: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05
50: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05
50: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05
50: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05
50: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05
50: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05
50: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05
50: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05
50: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05
50: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05
50: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05
50: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05
50: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05
50: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05
50: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05
50: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05
50: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02
50: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02
50: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02
50: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02
50: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02
50: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02
50: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02
50: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02
50: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02
50: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02
50: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02
50: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02
50: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02
50: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02
50: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02
50: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02
50: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02
50: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02
50: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02
50: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02
50: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02
50: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02
50: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02
50: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02
50: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2
50: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2
50: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2
50: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07
50: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06
50: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06
50: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06
50: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00
50: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07
50: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06
50: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08
50: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07
50: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06
50: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07
50: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06
50: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06
50: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06
50: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06
50: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07
50: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07
50: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07
50: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06
50: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06
50: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08
50: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07
50: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08
50: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06
50: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07
50: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05
50: reppow = 12
50: fudgeQQ = 0.5
50: cmap
50: atomtypes:
50: atomtype[ 0]={atomnumber= 7}
50: atomtype[ 1]={atomnumber= 1}
50: atomtype[ 2]={atomnumber= 6}
50: atomtype[ 3]={atomnumber= 1}
50: atomtype[ 4]={atomnumber= 6}
50: atomtype[ 5]={atomnumber= 8}
50: atomtype[ 6]={atomnumber= 6}
50: atomtype[ 7]={atomnumber= 1}
50: atomtype[ 8]={atomnumber= 6}
50: atomtype[ 9]={atomnumber= 16}
50: moltype (0):
50: name="Protein_chain_B"
50: atoms:
50: atom (156):
50: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
50: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6}
50: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
50: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
50: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
50: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6}
50: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
50: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6}
50: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8}
50: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7}
50: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1}
50: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6}
50: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6}
50: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
50: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
50: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6}
50: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8}
50: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7}
50: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1}
50: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6}
50: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
50: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6}
50: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
50: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
50: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6}
50: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8}
50: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7}
50: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1}
50: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6}
50: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
50: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
50: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6}
50: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8}
50: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1}
50: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6}
50: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6}
50: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6}
50: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6}
50: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1}
50: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6}
50: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6}
50: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8}
50: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7}
50: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1}
50: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6}
50: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
50: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6}
50: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
50: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
50: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16}
50: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1}
50: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6}
50: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8}
50: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7}
50: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1}
50: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6}
50: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6}
50: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6}
50: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6}
50: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
50: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
50: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6}
50: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8}
50: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7}
50: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1}
50: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6}
50: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6}
50: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6}
50: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
50: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
50: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6}
50: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8}
50: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7}
50: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1}
50: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6}
50: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6}
50: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6}
50: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8}
50: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7}
50: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1}
50: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6}
50: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6}
50: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6}
50: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8}
50: atom (156):
50: atom[0]={name="N"}
50: atom[1]={name="H1"}
50: atom[2]={name="H2"}
50: atom[3]={name="H3"}
50: atom[4]={name="CA"}
50: atom[5]={name="HA"}
50: atom[6]={name="CB"}
50: atom[7]={name="HB1"}
50: atom[8]={name="HB2"}
50: atom[9]={name="CG"}
50: atom[10]={name="HG1"}
50: atom[11]={name="HG2"}
50: atom[12]={name="CD"}
50: atom[13]={name="HD1"}
50: atom[14]={name="HD2"}
50: atom[15]={name="CE"}
50: atom[16]={name="HE1"}
50: atom[17]={name="HE2"}
50: atom[18]={name="NZ"}
50: atom[19]={name="HZ1"}
50: atom[20]={name="HZ2"}
50: atom[21]={name="HZ3"}
50: atom[22]={name="C"}
50: atom[23]={name="O"}
50: atom[24]={name="N"}
50: atom[25]={name="H"}
50: atom[26]={name="CA"}
50: atom[27]={name="HA"}
50: atom[28]={name="CB"}
50: atom[29]={name="HB"}
50: atom[30]={name="CG1"}
50: atom[31]={name="HG11"}
50: atom[32]={name="HG12"}
50: atom[33]={name="HG13"}
50: atom[34]={name="CG2"}
50: atom[35]={name="HG21"}
50: atom[36]={name="HG22"}
50: atom[37]={name="HG23"}
50: atom[38]={name="C"}
50: atom[39]={name="O"}
50: atom[40]={name="N"}
50: atom[41]={name="H"}
50: atom[42]={name="CA"}
50: atom[43]={name="HA"}
50: atom[44]={name="CB"}
50: atom[45]={name="HB1"}
50: atom[46]={name="HB2"}
50: atom[47]={name="CG"}
50: atom[48]={name="CD1"}
50: atom[49]={name="HD1"}
50: atom[50]={name="CD2"}
50: atom[51]={name="HD2"}
50: atom[52]={name="CE1"}
50: atom[53]={name="HE1"}
50: atom[54]={name="CE2"}
50: atom[55]={name="HE2"}
50: atom[56]={name="CZ"}
50: atom[57]={name="HZ"}
50: atom[58]={name="C"}
50: atom[59]={name="O"}
50: atom[60]={name="N"}
50: atom[61]={name="H"}
50: atom[62]={name="CA"}
50: atom[63]={name="HA1"}
50: atom[64]={name="HA2"}
50: atom[65]={name="C"}
50: atom[66]={name="O"}
50: atom[67]={name="N"}
50: atom[68]={name="H"}
50: atom[69]={name="CA"}
50: atom[70]={name="HA"}
50: atom[71]={name="CB"}
50: atom[72]={name="HB1"}
50: atom[73]={name="HB2"}
50: atom[74]={name="CG"}
50: atom[75]={name="HG1"}
50: atom[76]={name="HG2"}
50: atom[77]={name="CD"}
50: atom[78]={name="HD1"}
50: atom[79]={name="HD2"}
50: atom[80]={name="NE"}
50: atom[81]={name="HE"}
50: atom[82]={name="CZ"}
50: atom[83]={name="NH1"}
50: atom[84]={name="HH11"}
50: atom[85]={name="HH12"}
50: atom[86]={name="NH2"}
50: atom[87]={name="HH21"}
50: atom[88]={name="HH22"}
50: atom[89]={name="C"}
50: atom[90]={name="O"}
50: atom[91]={name="N"}
50: atom[92]={name="H"}
50: atom[93]={name="CA"}
50: atom[94]={name="HA"}
50: atom[95]={name="CB"}
50: atom[96]={name="HB1"}
50: atom[97]={name="HB2"}
50: atom[98]={name="SG"}
50: atom[99]={name="HG"}
50: atom[100]={name="C"}
50: atom[101]={name="O"}
50: atom[102]={name="N"}
50: atom[103]={name="H"}
50: atom[104]={name="CA"}
50: atom[105]={name="HA"}
50: atom[106]={name="CB"}
50: atom[107]={name="HB1"}
50: atom[108]={name="HB2"}
50: atom[109]={name="CG"}
50: atom[110]={name="HG1"}
50: atom[111]={name="HG2"}
50: atom[112]={name="CD"}
50: atom[113]={name="OE1"}
50: atom[114]={name="OE2"}
50: atom[115]={name="C"}
50: atom[116]={name="O"}
50: atom[117]={name="N"}
50: atom[118]={name="H"}
50: atom[119]={name="CA"}
50: atom[120]={name="HA"}
50: atom[121]={name="CB"}
50: atom[122]={name="HB1"}
50: atom[123]={name="HB2"}
50: atom[124]={name="CG"}
50: atom[125]={name="HG"}
50: atom[126]={name="CD1"}
50: atom[127]={name="HD11"}
50: atom[128]={name="HD12"}
50: atom[129]={name="HD13"}
50: atom[130]={name="CD2"}
50: atom[131]={name="HD21"}
50: atom[132]={name="HD22"}
50: atom[133]={name="HD23"}
50: atom[134]={name="C"}
50: atom[135]={name="O"}
50: atom[136]={name="N"}
50: atom[137]={name="H"}
50: atom[138]={name="CA"}
50: atom[139]={name="HA"}
50: atom[140]={name="CB"}
50: atom[141]={name="HB1"}
50: atom[142]={name="HB2"}
50: atom[143]={name="HB3"}
50: atom[144]={name="C"}
50: atom[145]={name="O"}
50: atom[146]={name="N"}
50: atom[147]={name="H"}
50: atom[148]={name="CA"}
50: atom[149]={name="HA"}
50: atom[150]={name="CB"}
50: atom[151]={name="HB1"}
50: atom[152]={name="HB2"}
50: atom[153]={name="HB3"}
50: atom[154]={name="C"}
50: atom[155]={name="O"}
50: type (156):
50: type[0]={name="opls_287",nameB="opls_287"}
50: type[1]={name="opls_290",nameB="opls_290"}
50: type[2]={name="opls_290",nameB="opls_290"}
50: type[3]={name="opls_290",nameB="opls_290"}
50: type[4]={name="opls_293B",nameB="opls_293B"}
50: type[5]={name="opls_140",nameB="opls_140"}
50: type[6]={name="opls_136",nameB="opls_136"}
50: type[7]={name="opls_140",nameB="opls_140"}
50: type[8]={name="opls_140",nameB="opls_140"}
50: type[9]={name="opls_136",nameB="opls_136"}
50: type[10]={name="opls_140",nameB="opls_140"}
50: type[11]={name="opls_140",nameB="opls_140"}
50: type[12]={name="opls_136",nameB="opls_136"}
50: type[13]={name="opls_140",nameB="opls_140"}
50: type[14]={name="opls_140",nameB="opls_140"}
50: type[15]={name="opls_292",nameB="opls_292"}
50: type[16]={name="opls_140",nameB="opls_140"}
50: type[17]={name="opls_140",nameB="opls_140"}
50: type[18]={name="opls_287",nameB="opls_287"}
50: type[19]={name="opls_290",nameB="opls_290"}
50: type[20]={name="opls_290",nameB="opls_290"}
50: type[21]={name="opls_290",nameB="opls_290"}
50: type[22]={name="opls_235",nameB="opls_235"}
50: type[23]={name="opls_236",nameB="opls_236"}
50: type[24]={name="opls_238",nameB="opls_238"}
50: type[25]={name="opls_241",nameB="opls_241"}
50: type[26]={name="opls_224B",nameB="opls_224B"}
50: type[27]={name="opls_140",nameB="opls_140"}
50: type[28]={name="opls_137",nameB="opls_137"}
50: type[29]={name="opls_140",nameB="opls_140"}
50: type[30]={name="opls_135",nameB="opls_135"}
50: type[31]={name="opls_140",nameB="opls_140"}
50: type[32]={name="opls_140",nameB="opls_140"}
50: type[33]={name="opls_140",nameB="opls_140"}
50: type[34]={name="opls_135",nameB="opls_135"}
50: type[35]={name="opls_140",nameB="opls_140"}
50: type[36]={name="opls_140",nameB="opls_140"}
50: type[37]={name="opls_140",nameB="opls_140"}
50: type[38]={name="opls_235",nameB="opls_235"}
50: type[39]={name="opls_236",nameB="opls_236"}
50: type[40]={name="opls_238",nameB="opls_238"}
50: type[41]={name="opls_241",nameB="opls_241"}
50: type[42]={name="opls_224B",nameB="opls_224B"}
50: type[43]={name="opls_140",nameB="opls_140"}
50: type[44]={name="opls_149",nameB="opls_149"}
50: type[45]={name="opls_140",nameB="opls_140"}
50: type[46]={name="opls_140",nameB="opls_140"}
50: type[47]={name="opls_145",nameB="opls_145"}
50: type[48]={name="opls_145",nameB="opls_145"}
50: type[49]={name="opls_146",nameB="opls_146"}
50: type[50]={name="opls_145",nameB="opls_145"}
50: type[51]={name="opls_146",nameB="opls_146"}
50: type[52]={name="opls_145",nameB="opls_145"}
50: type[53]={name="opls_146",nameB="opls_146"}
50: type[54]={name="opls_145",nameB="opls_145"}
50: type[55]={name="opls_146",nameB="opls_146"}
50: type[56]={name="opls_145",nameB="opls_145"}
50: type[57]={name="opls_146",nameB="opls_146"}
50: type[58]={name="opls_235",nameB="opls_235"}
50: type[59]={name="opls_236",nameB="opls_236"}
50: type[60]={name="opls_238",nameB="opls_238"}
50: type[61]={name="opls_241",nameB="opls_241"}
50: type[62]={name="opls_223B",nameB="opls_223B"}
50: type[63]={name="opls_140",nameB="opls_140"}
50: type[64]={name="opls_140",nameB="opls_140"}
50: type[65]={name="opls_235",nameB="opls_235"}
50: type[66]={name="opls_236",nameB="opls_236"}
50: type[67]={name="opls_238",nameB="opls_238"}
50: type[68]={name="opls_241",nameB="opls_241"}
50: type[69]={name="opls_224B",nameB="opls_224B"}
50: type[70]={name="opls_140",nameB="opls_140"}
50: type[71]={name="opls_136",nameB="opls_136"}
50: type[72]={name="opls_140",nameB="opls_140"}
50: type[73]={name="opls_140",nameB="opls_140"}
50: type[74]={name="opls_308",nameB="opls_308"}
50: type[75]={name="opls_140",nameB="opls_140"}
50: type[76]={name="opls_140",nameB="opls_140"}
50: type[77]={name="opls_307",nameB="opls_307"}
50: type[78]={name="opls_140",nameB="opls_140"}
50: type[79]={name="opls_140",nameB="opls_140"}
50: type[80]={name="opls_303",nameB="opls_303"}
50: type[81]={name="opls_304",nameB="opls_304"}
50: type[82]={name="opls_302",nameB="opls_302"}
50: type[83]={name="opls_300",nameB="opls_300"}
50: type[84]={name="opls_301",nameB="opls_301"}
50: type[85]={name="opls_301",nameB="opls_301"}
50: type[86]={name="opls_300",nameB="opls_300"}
50: type[87]={name="opls_301",nameB="opls_301"}
50: type[88]={name="opls_301",nameB="opls_301"}
50: type[89]={name="opls_235",nameB="opls_235"}
50: type[90]={name="opls_236",nameB="opls_236"}
50: type[91]={name="opls_238",nameB="opls_238"}
50: type[92]={name="opls_241",nameB="opls_241"}
50: type[93]={name="opls_224B",nameB="opls_224B"}
50: type[94]={name="opls_140",nameB="opls_140"}
50: type[95]={name="opls_206",nameB="opls_206"}
50: type[96]={name="opls_140",nameB="opls_140"}
50: type[97]={name="opls_140",nameB="opls_140"}
50: type[98]={name="opls_200",nameB="opls_200"}
50: type[99]={name="opls_204",nameB="opls_204"}
50: type[100]={name="opls_235",nameB="opls_235"}
50: type[101]={name="opls_236",nameB="opls_236"}
50: type[102]={name="opls_238",nameB="opls_238"}
50: type[103]={name="opls_241",nameB="opls_241"}
50: type[104]={name="opls_224B",nameB="opls_224B"}
50: type[105]={name="opls_140",nameB="opls_140"}
50: type[106]={name="opls_136",nameB="opls_136"}
50: type[107]={name="opls_140",nameB="opls_140"}
50: type[108]={name="opls_140",nameB="opls_140"}
50: type[109]={name="opls_274",nameB="opls_274"}
50: type[110]={name="opls_140",nameB="opls_140"}
50: type[111]={name="opls_140",nameB="opls_140"}
50: type[112]={name="opls_271",nameB="opls_271"}
50: type[113]={name="opls_272",nameB="opls_272"}
50: type[114]={name="opls_272",nameB="opls_272"}
50: type[115]={name="opls_235",nameB="opls_235"}
50: type[116]={name="opls_236",nameB="opls_236"}
50: type[117]={name="opls_238",nameB="opls_238"}
50: type[118]={name="opls_241",nameB="opls_241"}
50: type[119]={name="opls_224B",nameB="opls_224B"}
50: type[120]={name="opls_140",nameB="opls_140"}
50: type[121]={name="opls_136",nameB="opls_136"}
50: type[122]={name="opls_140",nameB="opls_140"}
50: type[123]={name="opls_140",nameB="opls_140"}
50: type[124]={name="opls_137",nameB="opls_137"}
50: type[125]={name="opls_140",nameB="opls_140"}
50: type[126]={name="opls_135",nameB="opls_135"}
50: type[127]={name="opls_140",nameB="opls_140"}
50: type[128]={name="opls_140",nameB="opls_140"}
50: type[129]={name="opls_140",nameB="opls_140"}
50: type[130]={name="opls_135",nameB="opls_135"}
50: type[131]={name="opls_140",nameB="opls_140"}
50: type[132]={name="opls_140",nameB="opls_140"}
50: type[133]={name="opls_140",nameB="opls_140"}
50: type[134]={name="opls_235",nameB="opls_235"}
50: type[135]={name="opls_236",nameB="opls_236"}
50: type[136]={name="opls_238",nameB="opls_238"}
50: type[137]={name="opls_241",nameB="opls_241"}
50: type[138]={name="opls_224B",nameB="opls_224B"}
50: type[139]={name="opls_140",nameB="opls_140"}
50: type[140]={name="opls_135",nameB="opls_135"}
50: type[141]={name="opls_140",nameB="opls_140"}
50: type[142]={name="opls_140",nameB="opls_140"}
50: type[143]={name="opls_140",nameB="opls_140"}
50: type[144]={name="opls_235",nameB="opls_235"}
50: type[145]={name="opls_236",nameB="opls_236"}
50: type[146]={name="opls_238",nameB="opls_238"}
50: type[147]={name="opls_241",nameB="opls_241"}
50: type[148]={name="opls_224B",nameB="opls_224B"}
50: type[149]={name="opls_140",nameB="opls_140"}
50: type[150]={name="opls_135",nameB="opls_135"}
50: type[151]={name="opls_140",nameB="opls_140"}
50: type[152]={name="opls_140",nameB="opls_140"}
50: type[153]={name="opls_140",nameB="opls_140"}
50: type[154]={name="opls_235",nameB="opls_235"}
50: type[155]={name="opls_236",nameB="opls_236"}
50: residue (10):
50: residue[0]={name="LYS", nr=1, ic=' '}
50: residue[1]={name="VAL", nr=2, ic=' '}
50: residue[2]={name="PHE", nr=3, ic=' '}
50: residue[3]={name="GLY", nr=4, ic=' '}
50: residue[4]={name="ARG", nr=5, ic=' '}
50: residue[5]={name="CYS", nr=6, ic=' '}
50: residue[6]={name="GLU", nr=7, ic=' '}
50: residue[7]={name="LEU", nr=8, ic=' '}
50: residue[8]={name="ALA", nr=9, ic=' '}
50: residue[9]={name="ALA", nr=10, ic=' '}
50: excls:
50: numLists=156
50: numElements=1828
50: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
50: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22}
50: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22}
50: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22}
50: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22,
50: 23, 24, 25, 26}
50: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
50: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
50: 14, 15, 22, 23, 24}
50: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
50: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
50: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
50: 16, 17, 18, 22}
50: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
50: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
50: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
50: 17, 18, 19, 20, 21}
50: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
50: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
50: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
50: 20, 21}
50: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
50: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
50: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
50: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21}
50: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21}
50: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21}
50: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25,
50: 26, 27, 28, 38}
50: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26}
50: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29,
50: 30, 34, 38, 39, 40}
50: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38}
50: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
50: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42}
50: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
50: 40}
50: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
50: 34, 35, 36, 37, 38, 39, 40}
50: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
50: 36, 37, 38}
50: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
50: 36, 37, 38}
50: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34}
50: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34}
50: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34}
50: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
50: 36, 37, 38}
50: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37}
50: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37}
50: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37}
50: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
50: 40, 41, 42, 43, 44, 58}
50: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42}
50: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44,
50: 45, 46, 47, 58, 59, 60}
50: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58}
50: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
50: 48, 50, 58, 59, 60, 61, 62}
50: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
50: 60}
50: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
50: 50, 51, 52, 54, 58, 59, 60}
50: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
50: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
50: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
50: 52, 53, 54, 55, 56, 58}
50: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
50: 54, 56, 57}
50: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56}
50: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54,
50: 55, 56, 57}
50: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56}
50: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57}
50: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57}
50: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57}
50: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57}
50: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57}
50: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57}
50: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
50: 60, 61, 62, 63, 64, 65}
50: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62}
50: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64,
50: 65, 66, 67}
50: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65}
50: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
50: 68, 69}
50: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67}
50: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67}
50: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
50: 70, 71, 89}
50: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69}
50: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
50: 72, 73, 74, 89, 90, 91}
50: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89}
50: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
50: 75, 76, 77, 89, 90, 91, 92, 93}
50: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
50: 91}
50: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
50: 77, 78, 79, 80, 89, 90, 91}
50: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
50: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
50: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
50: 79, 80, 81, 82, 89}
50: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
50: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
50: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
50: 81, 82, 83, 86}
50: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
50: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
50: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,
50: 84, 85, 86, 87, 88}
50: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86}
50: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86,
50: 87, 88}
50: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
50: excls[84][num=6]={80, 82, 83, 84, 85, 86}
50: excls[85][num=6]={80, 82, 83, 84, 85, 86}
50: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
50: excls[87][num=6]={80, 82, 83, 86, 87, 88}
50: excls[88][num=6]={80, 82, 83, 86, 87, 88}
50: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
50: 91, 92, 93, 94, 95, 100}
50: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93}
50: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95,
50: 96, 97, 98, 100, 101, 102}
50: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100}
50: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98,
50: 99, 100, 101, 102, 103, 104}
50: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101,
50: 102}
50: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100,
50: 101, 102}
50: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100}
50: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100}
50: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100}
50: excls[99][num=6]={93, 95, 96, 97, 98, 99}
50: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101,
50: 102, 103, 104, 105, 106, 115}
50: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104}
50: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105,
50: 106, 107, 108, 109, 115, 116, 117}
50: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115}
50: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107,
50: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119}
50: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109,
50: 115, 116, 117}
50: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109,
50: 110, 111, 112, 113, 114, 115, 116, 117}
50: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111,
50: 112, 115}
50: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111,
50: 112, 115}
50: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111,
50: 112, 113, 114, 115}
50: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113,
50: 114}
50: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113,
50: 114}
50: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113,
50: 114}
50: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114}
50: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114}
50: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109,
50: 115, 116, 117, 118, 119, 120, 121, 134}
50: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119}
50: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119,
50: 120, 121, 122, 123, 124, 134, 135, 136}
50: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134}
50: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122,
50: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138}
50: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124,
50: 134, 135, 136}
50: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124,
50: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136}
50: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126,
50: 130, 134}
50: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126,
50: 130, 134}
50: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126,
50: 127, 128, 129, 130, 131, 132, 133, 134}
50: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128,
50: 129, 130, 131, 132, 133}
50: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128,
50: 129, 130, 131, 132, 133}
50: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130}
50: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130}
50: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130}
50: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128,
50: 129, 130, 131, 132, 133}
50: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133}
50: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133}
50: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133}
50: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124,
50: 134, 135, 136, 137, 138, 139, 140, 144}
50: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138}
50: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138,
50: 139, 140, 141, 142, 143, 144, 145, 146}
50: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144}
50: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141,
50: 142, 143, 144, 145, 146, 147, 148}
50: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143,
50: 144, 145, 146}
50: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143,
50: 144, 145, 146}
50: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144}
50: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144}
50: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144}
50: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143,
50: 144, 145, 146, 147, 148, 149, 150, 154}
50: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148}
50: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148,
50: 149, 150, 151, 152, 153, 154, 155}
50: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154}
50: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151,
50: 152, 153, 154, 155}
50: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153,
50: 154, 155}
50: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153,
50: 154, 155}
50: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154}
50: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154}
50: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154}
50: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153,
50: 154, 155}
50: excls[155][num=6]={146, 148, 149, 150, 154, 155}
50: Bond:
50: nr: 468
50: iatoms:
50: 0 type=100 (BONDS) 0 1
50: 1 type=100 (BONDS) 0 2
50: 2 type=100 (BONDS) 0 3
50: 3 type=101 (BONDS) 0 4
50: 4 type=102 (BONDS) 4 5
50: 5 type=103 (BONDS) 4 6
50: 6 type=104 (BONDS) 4 22
50: 7 type=102 (BONDS) 6 7
50: 8 type=102 (BONDS) 6 8
50: 9 type=103 (BONDS) 6 9
50: 10 type=102 (BONDS) 9 10
50: 11 type=102 (BONDS) 9 11
50: 12 type=103 (BONDS) 9 12
50: 13 type=102 (BONDS) 12 13
50: 14 type=102 (BONDS) 12 14
50: 15 type=103 (BONDS) 12 15
50: 16 type=102 (BONDS) 15 16
50: 17 type=102 (BONDS) 15 17
50: 18 type=101 (BONDS) 15 18
50: 19 type=100 (BONDS) 18 19
50: 20 type=100 (BONDS) 18 20
50: 21 type=100 (BONDS) 18 21
50: 22 type=105 (BONDS) 22 23
50: 23 type=106 (BONDS) 22 24
50: 24 type=100 (BONDS) 24 25
50: 25 type=107 (BONDS) 24 26
50: 26 type=102 (BONDS) 26 27
50: 27 type=103 (BONDS) 26 28
50: 28 type=104 (BONDS) 26 38
50: 29 type=102 (BONDS) 28 29
50: 30 type=103 (BONDS) 28 30
50: 31 type=103 (BONDS) 28 34
50: 32 type=102 (BONDS) 30 31
50: 33 type=102 (BONDS) 30 32
50: 34 type=102 (BONDS) 30 33
50: 35 type=102 (BONDS) 34 35
50: 36 type=102 (BONDS) 34 36
50: 37 type=102 (BONDS) 34 37
50: 38 type=105 (BONDS) 38 39
50: 39 type=106 (BONDS) 38 40
50: 40 type=100 (BONDS) 40 41
50: 41 type=107 (BONDS) 40 42
50: 42 type=102 (BONDS) 42 43
50: 43 type=103 (BONDS) 42 44
50: 44 type=104 (BONDS) 42 58
50: 45 type=102 (BONDS) 44 45
50: 46 type=102 (BONDS) 44 46
50: 47 type=108 (BONDS) 44 47
50: 48 type=109 (BONDS) 47 48
50: 49 type=109 (BONDS) 47 50
50: 50 type=110 (BONDS) 48 49
50: 51 type=109 (BONDS) 48 52
50: 52 type=110 (BONDS) 50 51
50: 53 type=109 (BONDS) 50 54
50: 54 type=110 (BONDS) 52 53
50: 55 type=109 (BONDS) 52 56
50: 56 type=110 (BONDS) 54 55
50: 57 type=109 (BONDS) 54 56
50: 58 type=110 (BONDS) 56 57
50: 59 type=105 (BONDS) 58 59
50: 60 type=106 (BONDS) 58 60
50: 61 type=100 (BONDS) 60 61
50: 62 type=107 (BONDS) 60 62
50: 63 type=102 (BONDS) 62 63
50: 64 type=102 (BONDS) 62 64
50: 65 type=104 (BONDS) 62 65
50: 66 type=105 (BONDS) 65 66
50: 67 type=106 (BONDS) 65 67
50: 68 type=100 (BONDS) 67 68
50: 69 type=107 (BONDS) 67 69
50: 70 type=102 (BONDS) 69 70
50: 71 type=103 (BONDS) 69 71
50: 72 type=104 (BONDS) 69 89
50: 73 type=102 (BONDS) 71 72
50: 74 type=102 (BONDS) 71 73
50: 75 type=103 (BONDS) 71 74
50: 76 type=102 (BONDS) 74 75
50: 77 type=102 (BONDS) 74 76
50: 78 type=103 (BONDS) 74 77
50: 79 type=102 (BONDS) 77 78
50: 80 type=102 (BONDS) 77 79
50: 81 type=111 (BONDS) 77 80
50: 82 type=100 (BONDS) 80 81
50: 83 type=112 (BONDS) 80 82
50: 84 type=112 (BONDS) 82 83
50: 85 type=112 (BONDS) 82 86
50: 86 type=100 (BONDS) 83 84
50: 87 type=100 (BONDS) 83 85
50: 88 type=100 (BONDS) 86 87
50: 89 type=100 (BONDS) 86 88
50: 90 type=105 (BONDS) 89 90
50: 91 type=106 (BONDS) 89 91
50: 92 type=100 (BONDS) 91 92
50: 93 type=107 (BONDS) 91 93
50: 94 type=102 (BONDS) 93 94
50: 95 type=103 (BONDS) 93 95
50: 96 type=104 (BONDS) 93 100
50: 97 type=102 (BONDS) 95 96
50: 98 type=102 (BONDS) 95 97
50: 99 type=113 (BONDS) 95 98
50: 100 type=114 (BONDS) 98 99
50: 101 type=105 (BONDS) 100 101
50: 102 type=106 (BONDS) 100 102
50: 103 type=100 (BONDS) 102 103
50: 104 type=107 (BONDS) 102 104
50: 105 type=102 (BONDS) 104 105
50: 106 type=103 (BONDS) 104 106
50: 107 type=104 (BONDS) 104 115
50: 108 type=102 (BONDS) 106 107
50: 109 type=102 (BONDS) 106 108
50: 110 type=103 (BONDS) 106 109
50: 111 type=102 (BONDS) 109 110
50: 112 type=102 (BONDS) 109 111
50: 113 type=104 (BONDS) 109 112
50: 114 type=115 (BONDS) 112 113
50: 115 type=115 (BONDS) 112 114
50: 116 type=105 (BONDS) 115 116
50: 117 type=106 (BONDS) 115 117
50: 118 type=100 (BONDS) 117 118
50: 119 type=107 (BONDS) 117 119
50: 120 type=102 (BONDS) 119 120
50: 121 type=103 (BONDS) 119 121
50: 122 type=104 (BONDS) 119 134
50: 123 type=102 (BONDS) 121 122
50: 124 type=102 (BONDS) 121 123
50: 125 type=103 (BONDS) 121 124
50: 126 type=102 (BONDS) 124 125
50: 127 type=103 (BONDS) 124 126
50: 128 type=103 (BONDS) 124 130
50: 129 type=102 (BONDS) 126 127
50: 130 type=102 (BONDS) 126 128
50: 131 type=102 (BONDS) 126 129
50: 132 type=102 (BONDS) 130 131
50: 133 type=102 (BONDS) 130 132
50: 134 type=102 (BONDS) 130 133
50: 135 type=105 (BONDS) 134 135
50: 136 type=106 (BONDS) 134 136
50: 137 type=100 (BONDS) 136 137
50: 138 type=107 (BONDS) 136 138
50: 139 type=102 (BONDS) 138 139
50: 140 type=103 (BONDS) 138 140
50: 141 type=104 (BONDS) 138 144
50: 142 type=102 (BONDS) 140 141
50: 143 type=102 (BONDS) 140 142
50: 144 type=102 (BONDS) 140 143
50: 145 type=105 (BONDS) 144 145
50: 146 type=106 (BONDS) 144 146
50: 147 type=100 (BONDS) 146 147
50: 148 type=107 (BONDS) 146 148
50: 149 type=102 (BONDS) 148 149
50: 150 type=103 (BONDS) 148 150
50: 151 type=104 (BONDS) 148 154
50: 152 type=102 (BONDS) 150 151
50: 153 type=102 (BONDS) 150 152
50: 154 type=102 (BONDS) 150 153
50: 155 type=105 (BONDS) 154 155
50: G96Bond:
50: nr: 0
50: Morse:
50: nr: 0
50: Cubic Bonds:
50: nr: 0
50: Connect Bonds:
50: nr: 0
50: Harmonic Pot.:
50: nr: 0
50: FENE Bonds:
50: nr: 0
50: Tab. Bonds:
50: nr: 0
50: Tab. Bonds NC:
50: nr: 0
50: Restraint Pot.:
50: nr: 0
50: Angle:
50: nr: 1124
50: iatoms:
50: 0 type=116 (ANGLES) 1 0 2
50: 1 type=116 (ANGLES) 1 0 3
50: 2 type=116 (ANGLES) 1 0 4
50: 3 type=116 (ANGLES) 2 0 3
50: 4 type=116 (ANGLES) 2 0 4
50: 5 type=116 (ANGLES) 3 0 4
50: 6 type=116 (ANGLES) 0 4 5
50: 7 type=117 (ANGLES) 0 4 6
50: 8 type=117 (ANGLES) 0 4 22
50: 9 type=118 (ANGLES) 5 4 6
50: 10 type=116 (ANGLES) 5 4 22
50: 11 type=119 (ANGLES) 6 4 22
50: 12 type=118 (ANGLES) 4 6 7
50: 13 type=118 (ANGLES) 4 6 8
50: 14 type=120 (ANGLES) 4 6 9
50: 15 type=121 (ANGLES) 7 6 8
50: 16 type=118 (ANGLES) 7 6 9
50: 17 type=118 (ANGLES) 8 6 9
50: 18 type=118 (ANGLES) 6 9 10
50: 19 type=118 (ANGLES) 6 9 11
50: 20 type=120 (ANGLES) 6 9 12
50: 21 type=121 (ANGLES) 10 9 11
50: 22 type=118 (ANGLES) 10 9 12
50: 23 type=118 (ANGLES) 11 9 12
50: 24 type=118 (ANGLES) 9 12 13
50: 25 type=118 (ANGLES) 9 12 14
50: 26 type=120 (ANGLES) 9 12 15
50: 27 type=121 (ANGLES) 13 12 14
50: 28 type=118 (ANGLES) 13 12 15
50: 29 type=118 (ANGLES) 14 12 15
50: 30 type=118 (ANGLES) 12 15 16
50: 31 type=118 (ANGLES) 12 15 17
50: 32 type=117 (ANGLES) 12 15 18
50: 33 type=121 (ANGLES) 16 15 17
50: 34 type=116 (ANGLES) 16 15 18
50: 35 type=116 (ANGLES) 17 15 18
50: 36 type=116 (ANGLES) 15 18 19
50: 37 type=116 (ANGLES) 15 18 20
50: 38 type=116 (ANGLES) 15 18 21
50: 39 type=116 (ANGLES) 19 18 20
50: 40 type=116 (ANGLES) 19 18 21
50: 41 type=116 (ANGLES) 20 18 21
50: 42 type=122 (ANGLES) 4 22 23
50: 43 type=123 (ANGLES) 4 22 24
50: 44 type=124 (ANGLES) 23 22 24
50: 45 type=125 (ANGLES) 22 24 25
50: 46 type=126 (ANGLES) 22 24 26
50: 47 type=127 (ANGLES) 25 24 26
50: 48 type=116 (ANGLES) 24 26 27
50: 49 type=128 (ANGLES) 24 26 28
50: 50 type=129 (ANGLES) 24 26 38
50: 51 type=118 (ANGLES) 27 26 28
50: 52 type=116 (ANGLES) 27 26 38
50: 53 type=119 (ANGLES) 28 26 38
50: 54 type=118 (ANGLES) 26 28 29
50: 55 type=120 (ANGLES) 26 28 30
50: 56 type=120 (ANGLES) 26 28 34
50: 57 type=118 (ANGLES) 29 28 30
50: 58 type=118 (ANGLES) 29 28 34
50: 59 type=120 (ANGLES) 30 28 34
50: 60 type=118 (ANGLES) 28 30 31
50: 61 type=118 (ANGLES) 28 30 32
50: 62 type=118 (ANGLES) 28 30 33
50: 63 type=121 (ANGLES) 31 30 32
50: 64 type=121 (ANGLES) 31 30 33
50: 65 type=121 (ANGLES) 32 30 33
50: 66 type=118 (ANGLES) 28 34 35
50: 67 type=118 (ANGLES) 28 34 36
50: 68 type=118 (ANGLES) 28 34 37
50: 69 type=121 (ANGLES) 35 34 36
50: 70 type=121 (ANGLES) 35 34 37
50: 71 type=121 (ANGLES) 36 34 37
50: 72 type=122 (ANGLES) 26 38 39
50: 73 type=123 (ANGLES) 26 38 40
50: 74 type=124 (ANGLES) 39 38 40
50: 75 type=125 (ANGLES) 38 40 41
50: 76 type=126 (ANGLES) 38 40 42
50: 77 type=127 (ANGLES) 41 40 42
50: 78 type=116 (ANGLES) 40 42 43
50: 79 type=128 (ANGLES) 40 42 44
50: 80 type=129 (ANGLES) 40 42 58
50: 81 type=118 (ANGLES) 43 42 44
50: 82 type=116 (ANGLES) 43 42 58
50: 83 type=119 (ANGLES) 44 42 58
50: 84 type=118 (ANGLES) 42 44 45
50: 85 type=118 (ANGLES) 42 44 46
50: 86 type=130 (ANGLES) 42 44 47
50: 87 type=121 (ANGLES) 45 44 46
50: 88 type=116 (ANGLES) 45 44 47
50: 89 type=116 (ANGLES) 46 44 47
50: 90 type=131 (ANGLES) 44 47 48
50: 91 type=131 (ANGLES) 44 47 50
50: 92 type=132 (ANGLES) 48 47 50
50: 93 type=133 (ANGLES) 47 48 49
50: 94 type=132 (ANGLES) 47 48 52
50: 95 type=133 (ANGLES) 49 48 52
50: 96 type=133 (ANGLES) 47 50 51
50: 97 type=132 (ANGLES) 47 50 54
50: 98 type=133 (ANGLES) 51 50 54
50: 99 type=133 (ANGLES) 48 52 53
50: 100 type=132 (ANGLES) 48 52 56
50: 101 type=133 (ANGLES) 53 52 56
50: 102 type=133 (ANGLES) 50 54 55
50: 103 type=132 (ANGLES) 50 54 56
50: 104 type=133 (ANGLES) 55 54 56
50: 105 type=132 (ANGLES) 52 56 54
50: 106 type=133 (ANGLES) 52 56 57
50: 107 type=133 (ANGLES) 54 56 57
50: 108 type=122 (ANGLES) 42 58 59
50: 109 type=123 (ANGLES) 42 58 60
50: 110 type=124 (ANGLES) 59 58 60
50: 111 type=125 (ANGLES) 58 60 61
50: 112 type=126 (ANGLES) 58 60 62
50: 113 type=127 (ANGLES) 61 60 62
50: 114 type=116 (ANGLES) 60 62 63
50: 115 type=116 (ANGLES) 60 62 64
50: 116 type=129 (ANGLES) 60 62 65
50: 117 type=121 (ANGLES) 63 62 64
50: 118 type=116 (ANGLES) 63 62 65
50: 119 type=116 (ANGLES) 64 62 65
50: 120 type=122 (ANGLES) 62 65 66
50: 121 type=123 (ANGLES) 62 65 67
50: 122 type=124 (ANGLES) 66 65 67
50: 123 type=125 (ANGLES) 65 67 68
50: 124 type=126 (ANGLES) 65 67 69
50: 125 type=127 (ANGLES) 68 67 69
50: 126 type=116 (ANGLES) 67 69 70
50: 127 type=128 (ANGLES) 67 69 71
50: 128 type=129 (ANGLES) 67 69 89
50: 129 type=118 (ANGLES) 70 69 71
50: 130 type=116 (ANGLES) 70 69 89
50: 131 type=119 (ANGLES) 71 69 89
50: 132 type=118 (ANGLES) 69 71 72
50: 133 type=118 (ANGLES) 69 71 73
50: 134 type=120 (ANGLES) 69 71 74
50: 135 type=121 (ANGLES) 72 71 73
50: 136 type=118 (ANGLES) 72 71 74
50: 137 type=118 (ANGLES) 73 71 74
50: 138 type=118 (ANGLES) 71 74 75
50: 139 type=118 (ANGLES) 71 74 76
50: 140 type=120 (ANGLES) 71 74 77
50: 141 type=121 (ANGLES) 75 74 76
50: 142 type=118 (ANGLES) 75 74 77
50: 143 type=118 (ANGLES) 76 74 77
50: 144 type=118 (ANGLES) 74 77 78
50: 145 type=118 (ANGLES) 74 77 79
50: 146 type=117 (ANGLES) 74 77 80
50: 147 type=121 (ANGLES) 78 77 79
50: 148 type=116 (ANGLES) 78 77 80
50: 149 type=116 (ANGLES) 79 77 80
50: 150 type=134 (ANGLES) 77 80 81
50: 151 type=135 (ANGLES) 77 80 82
50: 152 type=133 (ANGLES) 81 80 82
50: 153 type=131 (ANGLES) 80 82 83
50: 154 type=131 (ANGLES) 80 82 86
50: 155 type=131 (ANGLES) 83 82 86
50: 156 type=133 (ANGLES) 82 83 84
50: 157 type=133 (ANGLES) 82 83 85
50: 158 type=133 (ANGLES) 84 83 85
50: 159 type=133 (ANGLES) 82 86 87
50: 160 type=133 (ANGLES) 82 86 88
50: 161 type=133 (ANGLES) 87 86 88
50: 162 type=122 (ANGLES) 69 89 90
50: 163 type=123 (ANGLES) 69 89 91
50: 164 type=124 (ANGLES) 90 89 91
50: 165 type=125 (ANGLES) 89 91 92
50: 166 type=126 (ANGLES) 89 91 93
50: 167 type=127 (ANGLES) 92 91 93
50: 168 type=116 (ANGLES) 91 93 94
50: 169 type=128 (ANGLES) 91 93 95
50: 170 type=129 (ANGLES) 91 93 100
50: 171 type=118 (ANGLES) 94 93 95
50: 172 type=116 (ANGLES) 94 93 100
50: 173 type=119 (ANGLES) 95 93 100
50: 174 type=118 (ANGLES) 93 95 96
50: 175 type=118 (ANGLES) 93 95 97
50: 176 type=136 (ANGLES) 93 95 98
50: 177 type=121 (ANGLES) 96 95 97
50: 178 type=116 (ANGLES) 96 95 98
50: 179 type=116 (ANGLES) 97 95 98
50: 180 type=137 (ANGLES) 95 98 99
50: 181 type=122 (ANGLES) 93 100 101
50: 182 type=123 (ANGLES) 93 100 102
50: 183 type=124 (ANGLES) 101 100 102
50: 184 type=125 (ANGLES) 100 102 103
50: 185 type=126 (ANGLES) 100 102 104
50: 186 type=127 (ANGLES) 103 102 104
50: 187 type=116 (ANGLES) 102 104 105
50: 188 type=128 (ANGLES) 102 104 106
50: 189 type=129 (ANGLES) 102 104 115
50: 190 type=118 (ANGLES) 105 104 106
50: 191 type=116 (ANGLES) 105 104 115
50: 192 type=119 (ANGLES) 106 104 115
50: 193 type=118 (ANGLES) 104 106 107
50: 194 type=118 (ANGLES) 104 106 108
50: 195 type=120 (ANGLES) 104 106 109
50: 196 type=121 (ANGLES) 107 106 108
50: 197 type=118 (ANGLES) 107 106 109
50: 198 type=118 (ANGLES) 108 106 109
50: 199 type=118 (ANGLES) 106 109 110
50: 200 type=118 (ANGLES) 106 109 111
50: 201 type=119 (ANGLES) 106 109 112
50: 202 type=121 (ANGLES) 110 109 111
50: 203 type=116 (ANGLES) 110 109 112
50: 204 type=116 (ANGLES) 111 109 112
50: 205 type=138 (ANGLES) 109 112 113
50: 206 type=138 (ANGLES) 109 112 114
50: 207 type=139 (ANGLES) 113 112 114
50: 208 type=122 (ANGLES) 104 115 116
50: 209 type=123 (ANGLES) 104 115 117
50: 210 type=124 (ANGLES) 116 115 117
50: 211 type=125 (ANGLES) 115 117 118
50: 212 type=126 (ANGLES) 115 117 119
50: 213 type=127 (ANGLES) 118 117 119
50: 214 type=116 (ANGLES) 117 119 120
50: 215 type=128 (ANGLES) 117 119 121
50: 216 type=129 (ANGLES) 117 119 134
50: 217 type=118 (ANGLES) 120 119 121
50: 218 type=116 (ANGLES) 120 119 134
50: 219 type=119 (ANGLES) 121 119 134
50: 220 type=118 (ANGLES) 119 121 122
50: 221 type=118 (ANGLES) 119 121 123
50: 222 type=120 (ANGLES) 119 121 124
50: 223 type=121 (ANGLES) 122 121 123
50: 224 type=118 (ANGLES) 122 121 124
50: 225 type=118 (ANGLES) 123 121 124
50: 226 type=118 (ANGLES) 121 124 125
50: 227 type=120 (ANGLES) 121 124 126
50: 228 type=120 (ANGLES) 121 124 130
50: 229 type=118 (ANGLES) 125 124 126
50: 230 type=118 (ANGLES) 125 124 130
50: 231 type=120 (ANGLES) 126 124 130
50: 232 type=118 (ANGLES) 124 126 127
50: 233 type=118 (ANGLES) 124 126 128
50: 234 type=118 (ANGLES) 124 126 129
50: 235 type=121 (ANGLES) 127 126 128
50: 236 type=121 (ANGLES) 127 126 129
50: 237 type=121 (ANGLES) 128 126 129
50: 238 type=118 (ANGLES) 124 130 131
50: 239 type=118 (ANGLES) 124 130 132
50: 240 type=118 (ANGLES) 124 130 133
50: 241 type=121 (ANGLES) 131 130 132
50: 242 type=121 (ANGLES) 131 130 133
50: 243 type=121 (ANGLES) 132 130 133
50: 244 type=122 (ANGLES) 119 134 135
50: 245 type=123 (ANGLES) 119 134 136
50: 246 type=124 (ANGLES) 135 134 136
50: 247 type=125 (ANGLES) 134 136 137
50: 248 type=126 (ANGLES) 134 136 138
50: 249 type=127 (ANGLES) 137 136 138
50: 250 type=116 (ANGLES) 136 138 139
50: 251 type=128 (ANGLES) 136 138 140
50: 252 type=129 (ANGLES) 136 138 144
50: 253 type=118 (ANGLES) 139 138 140
50: 254 type=116 (ANGLES) 139 138 144
50: 255 type=119 (ANGLES) 140 138 144
50: 256 type=118 (ANGLES) 138 140 141
50: 257 type=118 (ANGLES) 138 140 142
50: 258 type=118 (ANGLES) 138 140 143
50: 259 type=121 (ANGLES) 141 140 142
50: 260 type=121 (ANGLES) 141 140 143
50: 261 type=121 (ANGLES) 142 140 143
50: 262 type=122 (ANGLES) 138 144 145
50: 263 type=123 (ANGLES) 138 144 146
50: 264 type=124 (ANGLES) 145 144 146
50: 265 type=125 (ANGLES) 144 146 147
50: 266 type=126 (ANGLES) 144 146 148
50: 267 type=127 (ANGLES) 147 146 148
50: 268 type=116 (ANGLES) 146 148 149
50: 269 type=128 (ANGLES) 146 148 150
50: 270 type=129 (ANGLES) 146 148 154
50: 271 type=118 (ANGLES) 149 148 150
50: 272 type=116 (ANGLES) 149 148 154
50: 273 type=119 (ANGLES) 150 148 154
50: 274 type=118 (ANGLES) 148 150 151
50: 275 type=118 (ANGLES) 148 150 152
50: 276 type=118 (ANGLES) 148 150 153
50: 277 type=121 (ANGLES) 151 150 152
50: 278 type=121 (ANGLES) 151 150 153
50: 279 type=121 (ANGLES) 152 150 153
50: 280 type=122 (ANGLES) 148 154 155
50: G96Angle:
50: nr: 0
50: Restricted Angles:
50: nr: 0
50: Lin. Angle:
50: nr: 0
50: Bond-Cross:
50: nr: 0
50: BA-Cross:
50: nr: 0
50: U-B:
50: nr: 0
50: Quartic Angles:
50: nr: 0
50: Tab. Angles:
50: nr: 0
50: Proper Dih.:
50: nr: 145
50: iatoms:
50: 0 type=140 (PDIHS) 4 24 22 23
50: 1 type=141 (PDIHS) 22 26 24 25
50: 2 type=140 (PDIHS) 26 40 38 39
50: 3 type=141 (PDIHS) 38 42 40 41
50: 4 type=140 (PDIHS) 42 60 58 59
50: 5 type=142 (PDIHS) 44 47 50 48
50: 6 type=142 (PDIHS) 47 52 48 49
50: 7 type=142 (PDIHS) 47 54 50 51
50: 8 type=142 (PDIHS) 48 56 52 53
50: 9 type=142 (PDIHS) 50 56 54 55
50: 10 type=142 (PDIHS) 52 54 56 57
50: 11 type=141 (PDIHS) 58 62 60 61
50: 12 type=140 (PDIHS) 62 67 65 66
50: 13 type=141 (PDIHS) 65 69 67 68
50: 14 type=140 (PDIHS) 69 91 89 90
50: 15 type=141 (PDIHS) 77 82 80 81
50: 16 type=140 (PDIHS) 80 83 82 86
50: 17 type=141 (PDIHS) 82 84 83 85
50: 18 type=141 (PDIHS) 82 87 86 88
50: 19 type=141 (PDIHS) 89 93 91 92
50: 20 type=140 (PDIHS) 93 102 100 101
50: 21 type=141 (PDIHS) 100 104 102 103
50: 22 type=140 (PDIHS) 104 117 115 116
50: 23 type=140 (PDIHS) 109 113 112 114
50: 24 type=141 (PDIHS) 115 119 117 118
50: 25 type=140 (PDIHS) 119 136 134 135
50: 26 type=141 (PDIHS) 134 138 136 137
50: 27 type=140 (PDIHS) 138 146 144 145
50: 28 type=141 (PDIHS) 144 148 146 147
50: Ryckaert-Bell.:
50: nr: 1565
50: iatoms:
50: 0 type=143 (RBDIHS) 1 0 4 5
50: 1 type=144 (RBDIHS) 1 0 4 6
50: 2 type=144 (RBDIHS) 1 0 4 22
50: 3 type=143 (RBDIHS) 2 0 4 5
50: 4 type=144 (RBDIHS) 2 0 4 6
50: 5 type=144 (RBDIHS) 2 0 4 22
50: 6 type=143 (RBDIHS) 3 0 4 5
50: 7 type=144 (RBDIHS) 3 0 4 6
50: 8 type=144 (RBDIHS) 3 0 4 22
50: 9 type=145 (RBDIHS) 0 4 6 9
50: 10 type=146 (RBDIHS) 22 4 6 9
50: 11 type=147 (RBDIHS) 0 4 6 7
50: 12 type=147 (RBDIHS) 0 4 6 8
50: 13 type=148 (RBDIHS) 5 4 6 7
50: 14 type=148 (RBDIHS) 5 4 6 8
50: 15 type=148 (RBDIHS) 5 4 6 9
50: 16 type=149 (RBDIHS) 22 4 6 7
50: 17 type=149 (RBDIHS) 22 4 6 8
50: 18 type=150 (RBDIHS) 0 4 22 24
50: 19 type=151 (RBDIHS) 6 4 22 24
50: 20 type=148 (RBDIHS) 4 6 9 10
50: 21 type=148 (RBDIHS) 4 6 9 11
50: 22 type=152 (RBDIHS) 4 6 9 12
50: 23 type=148 (RBDIHS) 7 6 9 10
50: 24 type=148 (RBDIHS) 7 6 9 11
50: 25 type=148 (RBDIHS) 7 6 9 12
50: 26 type=148 (RBDIHS) 8 6 9 10
50: 27 type=148 (RBDIHS) 8 6 9 11
50: 28 type=148 (RBDIHS) 8 6 9 12
50: 29 type=148 (RBDIHS) 6 9 12 13
50: 30 type=148 (RBDIHS) 6 9 12 14
50: 31 type=152 (RBDIHS) 6 9 12 15
50: 32 type=148 (RBDIHS) 10 9 12 13
50: 33 type=148 (RBDIHS) 10 9 12 14
50: 34 type=148 (RBDIHS) 10 9 12 15
50: 35 type=148 (RBDIHS) 11 9 12 13
50: 36 type=148 (RBDIHS) 11 9 12 14
50: 37 type=148 (RBDIHS) 11 9 12 15
50: 38 type=148 (RBDIHS) 9 12 15 16
50: 39 type=148 (RBDIHS) 9 12 15 17
50: 40 type=153 (RBDIHS) 9 12 15 18
50: 41 type=148 (RBDIHS) 13 12 15 16
50: 42 type=148 (RBDIHS) 13 12 15 17
50: 43 type=154 (RBDIHS) 13 12 15 18
50: 44 type=148 (RBDIHS) 14 12 15 16
50: 45 type=148 (RBDIHS) 14 12 15 17
50: 46 type=154 (RBDIHS) 14 12 15 18
50: 47 type=144 (RBDIHS) 12 15 18 19
50: 48 type=144 (RBDIHS) 12 15 18 20
50: 49 type=144 (RBDIHS) 12 15 18 21
50: 50 type=143 (RBDIHS) 16 15 18 19
50: 51 type=143 (RBDIHS) 16 15 18 20
50: 52 type=143 (RBDIHS) 16 15 18 21
50: 53 type=143 (RBDIHS) 17 15 18 19
50: 54 type=143 (RBDIHS) 17 15 18 20
50: 55 type=143 (RBDIHS) 17 15 18 21
50: 56 type=155 (RBDIHS) 4 22 24 25
50: 57 type=156 (RBDIHS) 4 22 24 26
50: 58 type=155 (RBDIHS) 23 22 24 25
50: 59 type=157 (RBDIHS) 23 22 24 26
50: 60 type=158 (RBDIHS) 22 24 26 28
50: 61 type=159 (RBDIHS) 22 24 26 38
50: 62 type=160 (RBDIHS) 24 26 28 30
50: 63 type=160 (RBDIHS) 24 26 28 34
50: 64 type=161 (RBDIHS) 38 26 28 30
50: 65 type=161 (RBDIHS) 38 26 28 34
50: 66 type=147 (RBDIHS) 24 26 28 29
50: 67 type=148 (RBDIHS) 27 26 28 29
50: 68 type=148 (RBDIHS) 27 26 28 30
50: 69 type=148 (RBDIHS) 27 26 28 34
50: 70 type=149 (RBDIHS) 38 26 28 29
50: 71 type=150 (RBDIHS) 24 26 38 40
50: 72 type=151 (RBDIHS) 28 26 38 40
50: 73 type=148 (RBDIHS) 26 28 30 31
50: 74 type=148 (RBDIHS) 26 28 30 32
50: 75 type=148 (RBDIHS) 26 28 30 33
50: 76 type=148 (RBDIHS) 29 28 30 31
50: 77 type=148 (RBDIHS) 29 28 30 32
50: 78 type=148 (RBDIHS) 29 28 30 33
50: 79 type=148 (RBDIHS) 34 28 30 31
50: 80 type=148 (RBDIHS) 34 28 30 32
50: 81 type=148 (RBDIHS) 34 28 30 33
50: 82 type=148 (RBDIHS) 26 28 34 35
50: 83 type=148 (RBDIHS) 26 28 34 36
50: 84 type=148 (RBDIHS) 26 28 34 37
50: 85 type=148 (RBDIHS) 29 28 34 35
50: 86 type=148 (RBDIHS) 29 28 34 36
50: 87 type=148 (RBDIHS) 29 28 34 37
50: 88 type=148 (RBDIHS) 30 28 34 35
50: 89 type=148 (RBDIHS) 30 28 34 36
50: 90 type=148 (RBDIHS) 30 28 34 37
50: 91 type=155 (RBDIHS) 26 38 40 41
50: 92 type=156 (RBDIHS) 26 38 40 42
50: 93 type=155 (RBDIHS) 39 38 40 41
50: 94 type=157 (RBDIHS) 39 38 40 42
50: 95 type=158 (RBDIHS) 38 40 42 44
50: 96 type=159 (RBDIHS) 38 40 42 58
50: 97 type=147 (RBDIHS) 40 42 44 45
50: 98 type=147 (RBDIHS) 40 42 44 46
50: 99 type=162 (RBDIHS) 40 42 44 47
50: 100 type=148 (RBDIHS) 43 42 44 45
50: 101 type=148 (RBDIHS) 43 42 44 46
50: 102 type=163 (RBDIHS) 43 42 44 47
50: 103 type=149 (RBDIHS) 58 42 44 45
50: 104 type=149 (RBDIHS) 58 42 44 46
50: 105 type=164 (RBDIHS) 58 42 44 47
50: 106 type=150 (RBDIHS) 40 42 58 60
50: 107 type=151 (RBDIHS) 44 42 58 60
50: 108 type=165 (RBDIHS) 44 47 48 49
50: 109 type=165 (RBDIHS) 44 47 48 52
50: 110 type=165 (RBDIHS) 50 47 48 49
50: 111 type=165 (RBDIHS) 50 47 48 52
50: 112 type=165 (RBDIHS) 44 47 50 51
50: 113 type=165 (RBDIHS) 44 47 50 54
50: 114 type=165 (RBDIHS) 48 47 50 51
50: 115 type=165 (RBDIHS) 48 47 50 54
50: 116 type=165 (RBDIHS) 47 48 52 53
50: 117 type=165 (RBDIHS) 47 48 52 56
50: 118 type=165 (RBDIHS) 49 48 52 53
50: 119 type=165 (RBDIHS) 49 48 52 56
50: 120 type=165 (RBDIHS) 47 50 54 55
50: 121 type=165 (RBDIHS) 47 50 54 56
50: 122 type=165 (RBDIHS) 51 50 54 55
50: 123 type=165 (RBDIHS) 51 50 54 56
50: 124 type=165 (RBDIHS) 48 52 56 54
50: 125 type=165 (RBDIHS) 48 52 56 57
50: 126 type=165 (RBDIHS) 53 52 56 54
50: 127 type=165 (RBDIHS) 53 52 56 57
50: 128 type=165 (RBDIHS) 50 54 56 52
50: 129 type=165 (RBDIHS) 50 54 56 57
50: 130 type=165 (RBDIHS) 55 54 56 52
50: 131 type=165 (RBDIHS) 55 54 56 57
50: 132 type=155 (RBDIHS) 42 58 60 61
50: 133 type=156 (RBDIHS) 42 58 60 62
50: 134 type=155 (RBDIHS) 59 58 60 61
50: 135 type=157 (RBDIHS) 59 58 60 62
50: 136 type=159 (RBDIHS) 58 60 62 65
50: 137 type=150 (RBDIHS) 60 62 65 67
50: 138 type=155 (RBDIHS) 62 65 67 68
50: 139 type=156 (RBDIHS) 62 65 67 69
50: 140 type=155 (RBDIHS) 66 65 67 68
50: 141 type=157 (RBDIHS) 66 65 67 69
50: 142 type=158 (RBDIHS) 65 67 69 71
50: 143 type=159 (RBDIHS) 65 67 69 89
50: 144 type=166 (RBDIHS) 67 69 71 74
50: 145 type=167 (RBDIHS) 89 69 71 74
50: 146 type=147 (RBDIHS) 67 69 71 72
50: 147 type=147 (RBDIHS) 67 69 71 73
50: 148 type=148 (RBDIHS) 70 69 71 72
50: 149 type=148 (RBDIHS) 70 69 71 73
50: 150 type=148 (RBDIHS) 70 69 71 74
50: 151 type=149 (RBDIHS) 89 69 71 72
50: 152 type=149 (RBDIHS) 89 69 71 73
50: 153 type=150 (RBDIHS) 67 69 89 91
50: 154 type=151 (RBDIHS) 71 69 89 91
50: 155 type=148 (RBDIHS) 69 71 74 75
50: 156 type=148 (RBDIHS) 69 71 74 76
50: 157 type=152 (RBDIHS) 69 71 74 77
50: 158 type=148 (RBDIHS) 72 71 74 75
50: 159 type=148 (RBDIHS) 72 71 74 76
50: 160 type=148 (RBDIHS) 72 71 74 77
50: 161 type=148 (RBDIHS) 73 71 74 75
50: 162 type=148 (RBDIHS) 73 71 74 76
50: 163 type=148 (RBDIHS) 73 71 74 77
50: 164 type=148 (RBDIHS) 71 74 77 78
50: 165 type=148 (RBDIHS) 71 74 77 79
50: 166 type=153 (RBDIHS) 71 74 77 80
50: 167 type=148 (RBDIHS) 75 74 77 78
50: 168 type=148 (RBDIHS) 75 74 77 79
50: 169 type=168 (RBDIHS) 75 74 77 80
50: 170 type=148 (RBDIHS) 76 74 77 78
50: 171 type=148 (RBDIHS) 76 74 77 79
50: 172 type=168 (RBDIHS) 76 74 77 80
50: 173 type=169 (RBDIHS) 74 77 80 81
50: 174 type=170 (RBDIHS) 74 77 80 82
50: 175 type=171 (RBDIHS) 78 77 80 82
50: 176 type=171 (RBDIHS) 79 77 80 82
50: 177 type=172 (RBDIHS) 77 80 82 83
50: 178 type=172 (RBDIHS) 77 80 82 86
50: 179 type=173 (RBDIHS) 81 80 82 83
50: 180 type=173 (RBDIHS) 81 80 82 86
50: 181 type=173 (RBDIHS) 80 82 83 84
50: 182 type=173 (RBDIHS) 80 82 83 85
50: 183 type=173 (RBDIHS) 86 82 83 84
50: 184 type=173 (RBDIHS) 86 82 83 85
50: 185 type=173 (RBDIHS) 80 82 86 87
50: 186 type=173 (RBDIHS) 80 82 86 88
50: 187 type=173 (RBDIHS) 83 82 86 87
50: 188 type=173 (RBDIHS) 83 82 86 88
50: 189 type=155 (RBDIHS) 69 89 91 92
50: 190 type=156 (RBDIHS) 69 89 91 93
50: 191 type=155 (RBDIHS) 90 89 91 92
50: 192 type=157 (RBDIHS) 90 89 91 93
50: 193 type=158 (RBDIHS) 89 91 93 95
50: 194 type=159 (RBDIHS) 89 91 93 100
50: 195 type=174 (RBDIHS) 91 93 95 98
50: 196 type=175 (RBDIHS) 100 93 95 98
50: 197 type=147 (RBDIHS) 91 93 95 96
50: 198 type=147 (RBDIHS) 91 93 95 97
50: 199 type=148 (RBDIHS) 94 93 95 96
50: 200 type=148 (RBDIHS) 94 93 95 97
50: 201 type=176 (RBDIHS) 94 93 95 98
50: 202 type=149 (RBDIHS) 100 93 95 96
50: 203 type=149 (RBDIHS) 100 93 95 97
50: 204 type=150 (RBDIHS) 91 93 100 102
50: 205 type=151 (RBDIHS) 95 93 100 102
50: 206 type=177 (RBDIHS) 93 95 98 99
50: 207 type=178 (RBDIHS) 96 95 98 99
50: 208 type=178 (RBDIHS) 97 95 98 99
50: 209 type=155 (RBDIHS) 93 100 102 103
50: 210 type=156 (RBDIHS) 93 100 102 104
50: 211 type=155 (RBDIHS) 101 100 102 103
50: 212 type=157 (RBDIHS) 101 100 102 104
50: 213 type=158 (RBDIHS) 100 102 104 106
50: 214 type=159 (RBDIHS) 100 102 104 115
50: 215 type=179 (RBDIHS) 102 104 106 109
50: 216 type=180 (RBDIHS) 115 104 106 109
50: 217 type=147 (RBDIHS) 102 104 106 107
50: 218 type=147 (RBDIHS) 102 104 106 108
50: 219 type=148 (RBDIHS) 105 104 106 107
50: 220 type=148 (RBDIHS) 105 104 106 108
50: 221 type=148 (RBDIHS) 105 104 106 109
50: 222 type=149 (RBDIHS) 115 104 106 107
50: 223 type=149 (RBDIHS) 115 104 106 108
50: 224 type=150 (RBDIHS) 102 104 115 117
50: 225 type=151 (RBDIHS) 106 104 115 117
50: 226 type=148 (RBDIHS) 104 106 109 110
50: 227 type=148 (RBDIHS) 104 106 109 111
50: 228 type=181 (RBDIHS) 104 106 109 112
50: 229 type=148 (RBDIHS) 107 106 109 110
50: 230 type=148 (RBDIHS) 107 106 109 111
50: 231 type=182 (RBDIHS) 107 106 109 112
50: 232 type=148 (RBDIHS) 108 106 109 110
50: 233 type=148 (RBDIHS) 108 106 109 111
50: 234 type=182 (RBDIHS) 108 106 109 112
50: 235 type=183 (RBDIHS) 106 109 112 113
50: 236 type=183 (RBDIHS) 106 109 112 114
50: 237 type=155 (RBDIHS) 104 115 117 118
50: 238 type=156 (RBDIHS) 104 115 117 119
50: 239 type=155 (RBDIHS) 116 115 117 118
50: 240 type=157 (RBDIHS) 116 115 117 119
50: 241 type=158 (RBDIHS) 115 117 119 121
50: 242 type=159 (RBDIHS) 115 117 119 134
50: 243 type=184 (RBDIHS) 117 119 121 124
50: 244 type=185 (RBDIHS) 134 119 121 124
50: 245 type=147 (RBDIHS) 117 119 121 122
50: 246 type=147 (RBDIHS) 117 119 121 123
50: 247 type=148 (RBDIHS) 120 119 121 122
50: 248 type=148 (RBDIHS) 120 119 121 123
50: 249 type=148 (RBDIHS) 120 119 121 124
50: 250 type=149 (RBDIHS) 134 119 121 122
50: 251 type=149 (RBDIHS) 134 119 121 123
50: 252 type=150 (RBDIHS) 117 119 134 136
50: 253 type=151 (RBDIHS) 121 119 134 136
50: 254 type=148 (RBDIHS) 119 121 124 125
50: 255 type=152 (RBDIHS) 119 121 124 126
50: 256 type=152 (RBDIHS) 119 121 124 130
50: 257 type=148 (RBDIHS) 122 121 124 125
50: 258 type=148 (RBDIHS) 122 121 124 126
50: 259 type=148 (RBDIHS) 122 121 124 130
50: 260 type=148 (RBDIHS) 123 121 124 125
50: 261 type=148 (RBDIHS) 123 121 124 126
50: 262 type=148 (RBDIHS) 123 121 124 130
50: 263 type=148 (RBDIHS) 121 124 126 127
50: 264 type=148 (RBDIHS) 121 124 126 128
50: 265 type=148 (RBDIHS) 121 124 126 129
50: 266 type=148 (RBDIHS) 125 124 126 127
50: 267 type=148 (RBDIHS) 125 124 126 128
50: 268 type=148 (RBDIHS) 125 124 126 129
50: 269 type=148 (RBDIHS) 130 124 126 127
50: 270 type=148 (RBDIHS) 130 124 126 128
50: 271 type=148 (RBDIHS) 130 124 126 129
50: 272 type=148 (RBDIHS) 121 124 130 131
50: 273 type=148 (RBDIHS) 121 124 130 132
50: 274 type=148 (RBDIHS) 121 124 130 133
50: 275 type=148 (RBDIHS) 125 124 130 131
50: 276 type=148 (RBDIHS) 125 124 130 132
50: 277 type=148 (RBDIHS) 125 124 130 133
50: 278 type=148 (RBDIHS) 126 124 130 131
50: 279 type=148 (RBDIHS) 126 124 130 132
50: 280 type=148 (RBDIHS) 126 124 130 133
50: 281 type=155 (RBDIHS) 119 134 136 137
50: 282 type=156 (RBDIHS) 119 134 136 138
50: 283 type=155 (RBDIHS) 135 134 136 137
50: 284 type=157 (RBDIHS) 135 134 136 138
50: 285 type=158 (RBDIHS) 134 136 138 140
50: 286 type=159 (RBDIHS) 134 136 138 144
50: 287 type=147 (RBDIHS) 136 138 140 141
50: 288 type=147 (RBDIHS) 136 138 140 142
50: 289 type=147 (RBDIHS) 136 138 140 143
50: 290 type=148 (RBDIHS) 139 138 140 141
50: 291 type=148 (RBDIHS) 139 138 140 142
50: 292 type=148 (RBDIHS) 139 138 140 143
50: 293 type=149 (RBDIHS) 144 138 140 141
50: 294 type=149 (RBDIHS) 144 138 140 142
50: 295 type=149 (RBDIHS) 144 138 140 143
50: 296 type=150 (RBDIHS) 136 138 144 146
50: 297 type=151 (RBDIHS) 140 138 144 146
50: 298 type=155 (RBDIHS) 138 144 146 147
50: 299 type=156 (RBDIHS) 138 144 146 148
50: 300 type=155 (RBDIHS) 145 144 146 147
50: 301 type=157 (RBDIHS) 145 144 146 148
50: 302 type=158 (RBDIHS) 144 146 148 150
50: 303 type=159 (RBDIHS) 144 146 148 154
50: 304 type=147 (RBDIHS) 146 148 150 151
50: 305 type=147 (RBDIHS) 146 148 150 152
50: 306 type=147 (RBDIHS) 146 148 150 153
50: 307 type=148 (RBDIHS) 149 148 150 151
50: 308 type=148 (RBDIHS) 149 148 150 152
50: 309 type=148 (RBDIHS) 149 148 150 153
50: 310 type=149 (RBDIHS) 154 148 150 151
50: 311 type=149 (RBDIHS) 154 148 150 152
50: 312 type=149 (RBDIHS) 154 148 150 153
50: Restricted Dih.:
50: nr: 0
50: CBT Dih.:
50: nr: 0
50: Fourier Dih.:
50: nr: 0
50: Improper Dih.:
50: nr: 0
50: Improper Dih.:
50: nr: 0
50: Tab. Dih.:
50: nr: 0
50: CMAP Dih.:
50: nr: 0
50: GB 1-2 Pol. (unused):
50: nr: 0
50: GB 1-3 Pol. (unused):
50: nr: 0
50: GB 1-4 Pol. (unused):
50: nr: 0
50: GB Polarization (unused):
50: nr: 0
50: Nonpolar Sol. (unused):
50: nr: 0
50: LJ-14:
50: nr: 1197
50: iatoms:
50: 0 type=186 (LJ14) 0 7
50: 1 type=186 (LJ14) 0 8
50: 2 type=187 (LJ14) 0 9
50: 3 type=188 (LJ14) 0 23
50: 4 type=189 (LJ14) 0 24
50: 5 type=190 (LJ14) 1 5
50: 6 type=190 (LJ14) 1 6
50: 7 type=190 (LJ14) 1 22
50: 8 type=190 (LJ14) 2 5
50: 9 type=190 (LJ14) 2 6
50: 10 type=190 (LJ14) 2 22
50: 11 type=190 (LJ14) 3 5
50: 12 type=190 (LJ14) 3 6
50: 13 type=190 (LJ14) 3 22
50: 14 type=191 (LJ14) 4 10
50: 15 type=191 (LJ14) 4 11
50: 16 type=192 (LJ14) 4 12
50: 17 type=190 (LJ14) 4 25
50: 18 type=192 (LJ14) 4 26
50: 19 type=193 (LJ14) 5 7
50: 20 type=193 (LJ14) 5 8
50: 21 type=191 (LJ14) 5 9
50: 22 type=194 (LJ14) 5 23
50: 23 type=186 (LJ14) 5 24
50: 24 type=191 (LJ14) 6 13
50: 25 type=191 (LJ14) 6 14
50: 26 type=192 (LJ14) 6 15
50: 27 type=195 (LJ14) 6 23
50: 28 type=187 (LJ14) 6 24
50: 29 type=193 (LJ14) 7 10
50: 30 type=193 (LJ14) 7 11
50: 31 type=191 (LJ14) 7 12
50: 32 type=196 (LJ14) 7 22
50: 33 type=193 (LJ14) 8 10
50: 34 type=193 (LJ14) 8 11
50: 35 type=191 (LJ14) 8 12
50: 36 type=196 (LJ14) 8 22
50: 37 type=191 (LJ14) 9 16
50: 38 type=191 (LJ14) 9 17
50: 39 type=187 (LJ14) 9 18
50: 40 type=197 (LJ14) 9 22
50: 41 type=193 (LJ14) 10 13
50: 42 type=193 (LJ14) 10 14
50: 43 type=191 (LJ14) 10 15
50: 44 type=193 (LJ14) 11 13
50: 45 type=193 (LJ14) 11 14
50: 46 type=191 (LJ14) 11 15
50: 47 type=190 (LJ14) 12 19
50: 48 type=190 (LJ14) 12 20
50: 49 type=190 (LJ14) 12 21
50: 50 type=193 (LJ14) 13 16
50: 51 type=193 (LJ14) 13 17
50: 52 type=186 (LJ14) 13 18
50: 53 type=193 (LJ14) 14 16
50: 54 type=193 (LJ14) 14 17
50: 55 type=186 (LJ14) 14 18
50: 56 type=190 (LJ14) 16 19
50: 57 type=190 (LJ14) 16 20
50: 58 type=190 (LJ14) 16 21
50: 59 type=190 (LJ14) 17 19
50: 60 type=190 (LJ14) 17 20
50: 61 type=190 (LJ14) 17 21
50: 62 type=196 (LJ14) 22 27
50: 63 type=197 (LJ14) 22 28
50: 64 type=198 (LJ14) 22 38
50: 65 type=190 (LJ14) 23 25
50: 66 type=195 (LJ14) 23 26
50: 67 type=186 (LJ14) 24 29
50: 68 type=187 (LJ14) 24 30
50: 69 type=187 (LJ14) 24 34
50: 70 type=188 (LJ14) 24 39
50: 71 type=189 (LJ14) 24 40
50: 72 type=190 (LJ14) 25 27
50: 73 type=190 (LJ14) 25 28
50: 74 type=190 (LJ14) 25 38
50: 75 type=191 (LJ14) 26 31
50: 76 type=191 (LJ14) 26 32
50: 77 type=191 (LJ14) 26 33
50: 78 type=191 (LJ14) 26 35
50: 79 type=191 (LJ14) 26 36
50: 80 type=191 (LJ14) 26 37
50: 81 type=190 (LJ14) 26 41
50: 82 type=192 (LJ14) 26 42
50: 83 type=193 (LJ14) 27 29
50: 84 type=191 (LJ14) 27 30
50: 85 type=191 (LJ14) 27 34
50: 86 type=194 (LJ14) 27 39
50: 87 type=186 (LJ14) 27 40
50: 88 type=195 (LJ14) 28 39
50: 89 type=187 (LJ14) 28 40
50: 90 type=193 (LJ14) 29 31
50: 91 type=193 (LJ14) 29 32
50: 92 type=193 (LJ14) 29 33
50: 93 type=193 (LJ14) 29 35
50: 94 type=193 (LJ14) 29 36
50: 95 type=193 (LJ14) 29 37
50: 96 type=196 (LJ14) 29 38
50: 97 type=191 (LJ14) 30 35
50: 98 type=191 (LJ14) 30 36
50: 99 type=191 (LJ14) 30 37
50: 100 type=197 (LJ14) 30 38
50: 101 type=191 (LJ14) 31 34
50: 102 type=191 (LJ14) 32 34
50: 103 type=191 (LJ14) 33 34
50: 104 type=197 (LJ14) 34 38
50: 105 type=196 (LJ14) 38 43
50: 106 type=197 (LJ14) 38 44
50: 107 type=198 (LJ14) 38 58
50: 108 type=190 (LJ14) 39 41
50: 109 type=195 (LJ14) 39 42
50: 110 type=186 (LJ14) 40 45
50: 111 type=186 (LJ14) 40 46
50: 112 type=199 (LJ14) 40 47
50: 113 type=188 (LJ14) 40 59
50: 114 type=189 (LJ14) 40 60
50: 115 type=190 (LJ14) 41 43
50: 116 type=190 (LJ14) 41 44
50: 117 type=190 (LJ14) 41 58
50: 118 type=200 (LJ14) 42 48
50: 119 type=200 (LJ14) 42 50
50: 120 type=190 (LJ14) 42 61
50: 121 type=192 (LJ14) 42 62
50: 122 type=193 (LJ14) 43 45
50: 123 type=193 (LJ14) 43 46
50: 124 type=201 (LJ14) 43 47
50: 125 type=194 (LJ14) 43 59
50: 126 type=186 (LJ14) 43 60
50: 127 type=202 (LJ14) 44 49
50: 128 type=202 (LJ14) 44 51
50: 129 type=200 (LJ14) 44 52
50: 130 type=200 (LJ14) 44 54
50: 131 type=195 (LJ14) 44 59
50: 132 type=187 (LJ14) 44 60
50: 133 type=201 (LJ14) 45 48
50: 134 type=201 (LJ14) 45 50
50: 135 type=196 (LJ14) 45 58
50: 136 type=201 (LJ14) 46 48
50: 137 type=201 (LJ14) 46 50
50: 138 type=196 (LJ14) 46 58
50: 139 type=203 (LJ14) 47 53
50: 140 type=203 (LJ14) 47 55
50: 141 type=204 (LJ14) 47 56
50: 142 type=205 (LJ14) 47 58
50: 143 type=203 (LJ14) 48 51
50: 144 type=204 (LJ14) 48 54
50: 145 type=203 (LJ14) 48 57
50: 146 type=203 (LJ14) 49 50
50: 147 type=206 (LJ14) 49 53
50: 148 type=203 (LJ14) 49 56
50: 149 type=204 (LJ14) 50 52
50: 150 type=203 (LJ14) 50 57
50: 151 type=206 (LJ14) 51 55
50: 152 type=203 (LJ14) 51 56
50: 153 type=203 (LJ14) 52 55
50: 154 type=203 (LJ14) 53 54
50: 155 type=206 (LJ14) 53 57
50: 156 type=206 (LJ14) 55 57
50: 157 type=196 (LJ14) 58 63
50: 158 type=196 (LJ14) 58 64
50: 159 type=198 (LJ14) 58 65
50: 160 type=190 (LJ14) 59 61
50: 161 type=195 (LJ14) 59 62
50: 162 type=188 (LJ14) 60 66
50: 163 type=189 (LJ14) 60 67
50: 164 type=190 (LJ14) 61 63
50: 165 type=190 (LJ14) 61 64
50: 166 type=190 (LJ14) 61 65
50: 167 type=190 (LJ14) 62 68
50: 168 type=192 (LJ14) 62 69
50: 169 type=194 (LJ14) 63 66
50: 170 type=186 (LJ14) 63 67
50: 171 type=194 (LJ14) 64 66
50: 172 type=186 (LJ14) 64 67
50: 173 type=196 (LJ14) 65 70
50: 174 type=197 (LJ14) 65 71
50: 175 type=198 (LJ14) 65 89
50: 176 type=190 (LJ14) 66 68
50: 177 type=195 (LJ14) 66 69
50: 178 type=186 (LJ14) 67 72
50: 179 type=186 (LJ14) 67 73
50: 180 type=187 (LJ14) 67 74
50: 181 type=188 (LJ14) 67 90
50: 182 type=189 (LJ14) 67 91
50: 183 type=190 (LJ14) 68 70
50: 184 type=190 (LJ14) 68 71
50: 185 type=190 (LJ14) 68 89
50: 186 type=191 (LJ14) 69 75
50: 187 type=191 (LJ14) 69 76
50: 188 type=192 (LJ14) 69 77
50: 189 type=190 (LJ14) 69 92
50: 190 type=192 (LJ14) 69 93
50: 191 type=193 (LJ14) 70 72
50: 192 type=193 (LJ14) 70 73
50: 193 type=191 (LJ14) 70 74
50: 194 type=194 (LJ14) 70 90
50: 195 type=186 (LJ14) 70 91
50: 196 type=191 (LJ14) 71 78
50: 197 type=191 (LJ14) 71 79
50: 198 type=187 (LJ14) 71 80
50: 199 type=195 (LJ14) 71 90
50: 200 type=187 (LJ14) 71 91
50: 201 type=193 (LJ14) 72 75
50: 202 type=193 (LJ14) 72 76
50: 203 type=191 (LJ14) 72 77
50: 204 type=196 (LJ14) 72 89
50: 205 type=193 (LJ14) 73 75
50: 206 type=193 (LJ14) 73 76
50: 207 type=191 (LJ14) 73 77
50: 208 type=196 (LJ14) 73 89
50: 209 type=190 (LJ14) 74 81
50: 210 type=207 (LJ14) 74 82
50: 211 type=197 (LJ14) 74 89
50: 212 type=193 (LJ14) 75 78
50: 213 type=193 (LJ14) 75 79
50: 214 type=186 (LJ14) 75 80
50: 215 type=193 (LJ14) 76 78
50: 216 type=193 (LJ14) 76 79
50: 217 type=186 (LJ14) 76 80
50: 218 type=187 (LJ14) 77 83
50: 219 type=187 (LJ14) 77 86
50: 220 type=190 (LJ14) 78 81
50: 221 type=208 (LJ14) 78 82
50: 222 type=190 (LJ14) 79 81
50: 223 type=208 (LJ14) 79 82
50: 224 type=190 (LJ14) 80 84
50: 225 type=190 (LJ14) 80 85
50: 226 type=190 (LJ14) 80 87
50: 227 type=190 (LJ14) 80 88
50: 228 type=190 (LJ14) 81 83
50: 229 type=190 (LJ14) 81 86
50: 230 type=190 (LJ14) 83 87
50: 231 type=190 (LJ14) 83 88
50: 232 type=190 (LJ14) 84 86
50: 233 type=190 (LJ14) 85 86
50: 234 type=196 (LJ14) 89 94
50: 235 type=197 (LJ14) 89 95
50: 236 type=198 (LJ14) 89 100
50: 237 type=190 (LJ14) 90 92
50: 238 type=195 (LJ14) 90 93
50: 239 type=186 (LJ14) 91 96
50: 240 type=186 (LJ14) 91 97
50: 241 type=209 (LJ14) 91 98
50: 242 type=188 (LJ14) 91 101
50: 243 type=189 (LJ14) 91 102
50: 244 type=190 (LJ14) 92 94
50: 245 type=190 (LJ14) 92 95
50: 246 type=190 (LJ14) 92 100
50: 247 type=190 (LJ14) 93 99
50: 248 type=190 (LJ14) 93 103
50: 249 type=192 (LJ14) 93 104
50: 250 type=193 (LJ14) 94 96
50: 251 type=193 (LJ14) 94 97
50: 252 type=210 (LJ14) 94 98
50: 253 type=194 (LJ14) 94 101
50: 254 type=186 (LJ14) 94 102
50: 255 type=195 (LJ14) 95 101
50: 256 type=187 (LJ14) 95 102
50: 257 type=190 (LJ14) 96 99
50: 258 type=196 (LJ14) 96 100
50: 259 type=190 (LJ14) 97 99
50: 260 type=196 (LJ14) 97 100
50: 261 type=211 (LJ14) 98 100
50: 262 type=196 (LJ14) 100 105
50: 263 type=197 (LJ14) 100 106
50: 264 type=198 (LJ14) 100 115
50: 265 type=190 (LJ14) 101 103
50: 266 type=195 (LJ14) 101 104
50: 267 type=186 (LJ14) 102 107
50: 268 type=186 (LJ14) 102 108
50: 269 type=187 (LJ14) 102 109
50: 270 type=188 (LJ14) 102 116
50: 271 type=189 (LJ14) 102 117
50: 272 type=190 (LJ14) 103 105
50: 273 type=190 (LJ14) 103 106
50: 274 type=190 (LJ14) 103 115
50: 275 type=191 (LJ14) 104 110
50: 276 type=191 (LJ14) 104 111
50: 277 type=197 (LJ14) 104 112
50: 278 type=190 (LJ14) 104 118
50: 279 type=192 (LJ14) 104 119
50: 280 type=193 (LJ14) 105 107
50: 281 type=193 (LJ14) 105 108
50: 282 type=191 (LJ14) 105 109
50: 283 type=194 (LJ14) 105 116
50: 284 type=186 (LJ14) 105 117
50: 285 type=195 (LJ14) 106 113
50: 286 type=195 (LJ14) 106 114
50: 287 type=195 (LJ14) 106 116
50: 288 type=187 (LJ14) 106 117
50: 289 type=193 (LJ14) 107 110
50: 290 type=193 (LJ14) 107 111
50: 291 type=196 (LJ14) 107 112
50: 292 type=196 (LJ14) 107 115
50: 293 type=193 (LJ14) 108 110
50: 294 type=193 (LJ14) 108 111
50: 295 type=196 (LJ14) 108 112
50: 296 type=196 (LJ14) 108 115
50: 297 type=197 (LJ14) 109 115
50: 298 type=194 (LJ14) 110 113
50: 299 type=194 (LJ14) 110 114
50: 300 type=194 (LJ14) 111 113
50: 301 type=194 (LJ14) 111 114
50: 302 type=196 (LJ14) 115 120
50: 303 type=197 (LJ14) 115 121
50: 304 type=198 (LJ14) 115 134
50: 305 type=190 (LJ14) 116 118
50: 306 type=195 (LJ14) 116 119
50: 307 type=186 (LJ14) 117 122
50: 308 type=186 (LJ14) 117 123
50: 309 type=187 (LJ14) 117 124
50: 310 type=188 (LJ14) 117 135
50: 311 type=189 (LJ14) 117 136
50: 312 type=190 (LJ14) 118 120
50: 313 type=190 (LJ14) 118 121
50: 314 type=190 (LJ14) 118 134
50: 315 type=191 (LJ14) 119 125
50: 316 type=192 (LJ14) 119 126
50: 317 type=192 (LJ14) 119 130
50: 318 type=190 (LJ14) 119 137
50: 319 type=192 (LJ14) 119 138
50: 320 type=193 (LJ14) 120 122
50: 321 type=193 (LJ14) 120 123
50: 322 type=191 (LJ14) 120 124
50: 323 type=194 (LJ14) 120 135
50: 324 type=186 (LJ14) 120 136
50: 325 type=191 (LJ14) 121 127
50: 326 type=191 (LJ14) 121 128
50: 327 type=191 (LJ14) 121 129
50: 328 type=191 (LJ14) 121 131
50: 329 type=191 (LJ14) 121 132
50: 330 type=191 (LJ14) 121 133
50: 331 type=195 (LJ14) 121 135
50: 332 type=187 (LJ14) 121 136
50: 333 type=193 (LJ14) 122 125
50: 334 type=191 (LJ14) 122 126
50: 335 type=191 (LJ14) 122 130
50: 336 type=196 (LJ14) 122 134
50: 337 type=193 (LJ14) 123 125
50: 338 type=191 (LJ14) 123 126
50: 339 type=191 (LJ14) 123 130
50: 340 type=196 (LJ14) 123 134
50: 341 type=197 (LJ14) 124 134
50: 342 type=193 (LJ14) 125 127
50: 343 type=193 (LJ14) 125 128
50: 344 type=193 (LJ14) 125 129
50: 345 type=193 (LJ14) 125 131
50: 346 type=193 (LJ14) 125 132
50: 347 type=193 (LJ14) 125 133
50: 348 type=191 (LJ14) 126 131
50: 349 type=191 (LJ14) 126 132
50: 350 type=191 (LJ14) 126 133
50: 351 type=191 (LJ14) 127 130
50: 352 type=191 (LJ14) 128 130
50: 353 type=191 (LJ14) 129 130
50: 354 type=196 (LJ14) 134 139
50: 355 type=197 (LJ14) 134 140
50: 356 type=198 (LJ14) 134 144
50: 357 type=190 (LJ14) 135 137
50: 358 type=195 (LJ14) 135 138
50: 359 type=186 (LJ14) 136 141
50: 360 type=186 (LJ14) 136 142
50: 361 type=186 (LJ14) 136 143
50: 362 type=188 (LJ14) 136 145
50: 363 type=189 (LJ14) 136 146
50: 364 type=190 (LJ14) 137 139
50: 365 type=190 (LJ14) 137 140
50: 366 type=190 (LJ14) 137 144
50: 367 type=190 (LJ14) 138 147
50: 368 type=192 (LJ14) 138 148
50: 369 type=193 (LJ14) 139 141
50: 370 type=193 (LJ14) 139 142
50: 371 type=193 (LJ14) 139 143
50: 372 type=194 (LJ14) 139 145
50: 373 type=186 (LJ14) 139 146
50: 374 type=195 (LJ14) 140 145
50: 375 type=187 (LJ14) 140 146
50: 376 type=196 (LJ14) 141 144
50: 377 type=196 (LJ14) 142 144
50: 378 type=196 (LJ14) 143 144
50: 379 type=196 (LJ14) 144 149
50: 380 type=197 (LJ14) 144 150
50: 381 type=198 (LJ14) 144 154
50: 382 type=190 (LJ14) 145 147
50: 383 type=195 (LJ14) 145 148
50: 384 type=186 (LJ14) 146 151
50: 385 type=186 (LJ14) 146 152
50: 386 type=186 (LJ14) 146 153
50: 387 type=188 (LJ14) 146 155
50: 388 type=190 (LJ14) 147 149
50: 389 type=190 (LJ14) 147 150
50: 390 type=190 (LJ14) 147 154
50: 391 type=193 (LJ14) 149 151
50: 392 type=193 (LJ14) 149 152
50: 393 type=193 (LJ14) 149 153
50: 394 type=194 (LJ14) 149 155
50: 395 type=195 (LJ14) 150 155
50: 396 type=196 (LJ14) 151 154
50: 397 type=196 (LJ14) 152 154
50: 398 type=196 (LJ14) 153 154
50: Coulomb-14:
50: nr: 0
50: LJC-14 q:
50: nr: 0
50: LJC Pairs NB:
50: nr: 0
50: LJ (SR):
50: nr: 0
50: Buck.ham (SR):
50: nr: 0
50: LJ (unused):
50: nr: 0
50: B.ham (unused):
50: nr: 0
50: Disper. corr.:
50: nr: 0
50: Coulomb (SR):
50: nr: 0
50: Coul (unused):
50: nr: 0
50: RF excl.:
50: nr: 0
50: Coul. recip.:
50: nr: 0
50: LJ recip.:
50: nr: 0
50: DPD:
50: nr: 0
50: Polarization:
50: nr: 0
50: Water Pol.:
50: nr: 0
50: Thole Pol.:
50: nr: 0
50: Anharm. Pol.:
50: nr: 0
50: Position Rest.:
50: nr: 0
50: Flat-bottom posres:
50: nr: 0
50: Dis. Rest.:
50: nr: 0
50: D.R.Viol. (nm):
50: nr: 0
50: Orient. Rest.:
50: nr: 0
50: Ori. R. RMSD:
50: nr: 0
50: Angle Rest.:
50: nr: 0
50: Angle Rest. Z:
50: nr: 0
50: Dih. Rest.:
50: nr: 0
50: Dih. Rest. Viol.:
50: nr: 0
50: Constraint:
50: nr: 0
50: Constr. No Conn.:
50: nr: 0
50: Settle:
50: nr: 0
50: Virtual site 1:
50: nr: 0
50: Virtual site 2:
50: nr: 0
50: Virtual site 2fd:
50: nr: 0
50: Virtual site 3:
50: nr: 0
50: Virtual site 3fd:
50: nr: 0
50: Virtual site 3fad:
50: nr: 0
50: Virtual site 3out:
50: nr: 0
50: Virtual site 4fd:
50: nr: 0
50: Virtual site 4fdn:
50: nr: 0
50: Virtual site N:
50: nr: 0
50: COM Pull En.:
50: nr: 0
50: Density fitting:
50: nr: 0
50: Quantum En.:
50: nr: 0
50: Potential:
50: nr: 0
50: Kinetic En.:
50: nr: 0
50: Total Energy:
50: nr: 0
50: Conserved En.:
50: nr: 0
50: Temperature:
50: nr: 0
50: Vir. Temp. (not used):
50: nr: 0
50: Pres. DC:
50: nr: 0
50: Pressure:
50: nr: 0
50: dH/dl constr.:
50: nr: 0
50: dVremain/dl:
50: nr: 0
50: dEkin/dl:
50: nr: 0
50: dVcoul/dl:
50: nr: 0
50: dVvdw/dl:
50: nr: 0
50: dVbonded/dl:
50: nr: 0
50: dVrestraint/dl:
50: nr: 0
50: dVtemperature/dl:
50: nr: 0
50: grp[T-Coupling ] nr=1, name=[ rest]
50: grp[Energy Mon. ] nr=1, name=[ rest]
50: grp[Acceleration] nr=1, name=[ rest]
50: grp[Freeze ] nr=1, name=[ rest]
50: grp[User1 ] nr=1, name=[ rest]
50: grp[User2 ] nr=1, name=[ rest]
50: grp[VCM ] nr=1, name=[ rest]
50: grp[Compressed X] nr=1, name=[ rest]
50: grp[Or. Res. Fit] nr=1, name=[ rest]
50: grp[QMMM ] nr=1, name=[ rest]
50: grpname (11):
50: grpname[0]={name="System"}
50: grpname[1]={name="Protein"}
50: grpname[2]={name="Protein-H"}
50: grpname[3]={name="C-alpha"}
50: grpname[4]={name="Backbone"}
50: grpname[5]={name="MainChain"}
50: grpname[6]={name="MainChain+Cb"}
50: grpname[7]={name="MainChain+H"}
50: grpname[8]={name="SideChain"}
50: grpname[9]={name="SideChain-H"}
50: grpname[10]={name="rest"}
50: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM
50: allocated 0 0 0 0 0 0 0 0 0 0
50: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0
50: box (3x3):
50: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00}
50: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00}
50: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00}
50: box_rel (3x3):
50: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: boxv (3x3):
50: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: pres_prev (3x3):
50: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: svir_prev (3x3):
50: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: fvir_prev (3x3):
50: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: nosehoover_xi: not available
50: x (156x3):
50: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00}
50: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00}
50: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00}
50: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00}
50: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00}
50: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00}
50: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00}
50: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00}
50: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01}
50: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01}
50: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01}
50: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00}
50: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01}
50: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01}
50: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01}
50: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01}
50: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01}
50: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01}
50: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01}
50: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01}
50: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01}
50: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01}
50: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00}
50: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00}
50: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00}
50: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00}
50: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00}
50: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01}
50: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00}
50: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00}
50: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00}
50: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00}
50: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01}
50: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01}
50: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00}
50: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00}
50: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00}
50: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00}
50: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01}
50: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01}
50: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01}
50: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01}
50: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01}
50: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01}
50: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01}
50: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01}
50: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01}
50: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01}
50: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01}
50: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01}
50: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01}
50: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01}
50: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01}
50: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01}
50: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01}
50: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01}
50: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01}
50: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01}
50: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01}
50: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01}
50: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01}
50: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01}
50: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01}
50: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01}
50: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01}
50: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01}
50: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01}
50: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01}
50: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01}
50: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01}
50: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01}
50: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01}
50: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01}
50: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01}
50: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02}
50: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02}
50: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02}
50: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02}
50: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02}
50: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01}
50: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02}
50: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01}
50: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02}
50: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01}
50: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01}
50: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01}
50: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02}
50: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01}
50: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02}
50: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01}
50: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02}
50: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01}
50: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01}
50: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02}
50: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02}
50: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02}
50: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01}
50: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02}
50: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02}
50: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02}
50: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02}
50: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02}
50: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01}
50: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01}
50: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01}
50: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01}
50: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01}
50: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01}
50: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01}
50: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01}
50: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01}
50: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01}
50: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01}
50: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01}
50: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01}
50: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01}
50: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01}
50: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01}
50: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01}
50: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01}
50: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01}
50: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01}
50: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01}
50: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01}
50: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01}
50: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02}
50: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01}
50: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01}
50: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01}
50: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01}
50: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01}
50: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01}
50: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01}
50: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01}
50: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02}
50: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02}
50: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02}
50: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02}
50: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01}
50: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01}
50: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01}
50: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01}
50: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01}
50: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01}
50: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01}
50: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01}
50: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01}
50: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01}
50: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01}
50: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01}
50: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01}
50: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01}
50: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01}
50: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02}
50: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01}
50: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01}
50: v (156x3):
50: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: Group statistics
50: T-Coupling : 156 (total 156 atoms)
50: Energy Mon. : 156 (total 156 atoms)
50: Acceleration: 156 (total 156 atoms)
50: Freeze : 156 (total 156 atoms)
50: User1 : 156 (total 156 atoms)
50: User2 : 156 (total 156 atoms)
50: VCM : 156 (total 156 atoms)
50: Compressed X: 156 (total 156 atoms)
50: Or. Res. Fit: 156 (total 156 atoms)
50: QMMM : 156 (total 156 atoms)
50: [ OK ] DumpTest.WorksWithTpr (42 ms)
50: [ RUN ] DumpTest.WorksWithTprAndMdpWriting
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
50: [ OK ] DumpTest.WorksWithTprAndMdpWriting (8 ms)
50: [----------] 2 tests from DumpTest (53 ms total)
50:
50: [----------] 3 tests from HelpwritingTest
50: [ RUN ] HelpwritingTest.ConvertTprWritesHelp
50: [ OK ] HelpwritingTest.ConvertTprWritesHelp (37 ms)
50: [ RUN ] HelpwritingTest.DumpWritesHelp
50: [ OK ] HelpwritingTest.DumpWritesHelp (15 ms)
50: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp
50: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (2 ms)
50: [----------] 3 tests from HelpwritingTest (54 ms total)
50:
50: [----------] 4 tests from ReportMethodsTest
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
50: For a correct single-point energy evaluation with nsteps = 0, use
50: continuation = yes to avoid constraining the input coordinates.
50:
50: Generating 1-4 interactions: fudge = 0.5
50:
50: NOTE 2 [file lysozyme.top, line 1465]:
50: System has non-zero total charge: 2.000000
50: Total charge should normally be an integer. See
50: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
50: for discussion on how close it should be to an integer.
50:
50:
50:
50: Number of degrees of freedom in T-Coupling group rest is 465.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
50: NVE simulation with an initial temperature of zero: will use a Verlet
50: buffer of 10%. Check your energy drift!
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Setting the LD random seed to 1463155551
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50:
50: Generated 330891 of the 330891 1-4 parameter combinations
50:
50: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
50: Analysing residue names:
50: There are: 10 Protein residues
50: Analysing Protein...
50:
50: This run will generate roughly 0 Mb of data
50: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
50: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (1 ms)
50: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
50: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (1 ms)
50: [ RUN ] ReportMethodsTest.WritesCorrectInformation
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
50: [ OK ] ReportMethodsTest.WritesCorrectInformation (4 ms)
50: [ RUN ] ReportMethodsTest.ToolEndToEndTest
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
50: section: Methods
50: subsection: Simulation system
50: A system of 1 molecules (156 atoms) was simulated.
50:
50: subsection: Simulation settings
50: A total of 0 ns were simulated with a time step of 1 fs.
50: Neighbor searching was performed every 10 steps.
50: The Cut-off algorithm was used for electrostatic interactions.
50: with a cut-off of 1 nm.
50: A single cut-off of 1.1 nm was used for Van der Waals interactions.
50: [ OK ] ReportMethodsTest.ToolEndToEndTest (5 ms)
50: [----------] 4 tests from ReportMethodsTest (11 ms total)
50:
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: trr version: GMX_trn_file (single precision)
50:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (16 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (16 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (14 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from gro file '', 6 atoms.
50:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (16 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
50: -> frame 0 time 0.000
't= 0.00000', 6 atoms
50:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (15 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (15 ms)
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (92 ms total)
50:
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (4 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (6 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (5 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from gro file '', 6 atoms.
50:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (5 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
50: -> frame 0 time 0.000
't= 0.00000', 6 atoms
50:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (5 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (5 ms)
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (31 ms total)
50:
50: [----------] Global test environment tear-down
50: [==========] 21 tests from 5 test cases ran. (7317 ms total)
50: [ PASSED ] 21 tests.
50/65 Test #50: ToolUnitTests ......................... Passed 7.40 sec
test 51
Start 51: FileIOTests
51: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FileIOTests.xml"
51: Test timeout computed to be: 30
51: [==========] Running 42 tests from 10 test cases.
51: [----------] Global test environment set-up.
51: [----------] 4 tests from Checkpoint
51: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent
51: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (2 ms)
51: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent
51: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms)
51: [ RUN ] Checkpoint.KvtRoundTripInt64
51: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms)
51: [ RUN ] Checkpoint.KvtRoundTripReal
51: [ OK ] Checkpoint.KvtRoundTripReal (1 ms)
51: [----------] 4 tests from Checkpoint (3 ms total)
51:
51: [----------] 2 tests from FileMD5Test
51: [ RUN ] FileMD5Test.CanComputeMD5
51: [ OK ] FileMD5Test.CanComputeMD5 (5 ms)
51: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
51: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (2 ms)
51: [----------] 2 tests from FileMD5Test (8 ms total)
51:
51: [----------] 3 tests from MrcSerializer
51: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet
51: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms)
51: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize
51: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (1 ms)
51: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip
51: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (4 ms)
51: [----------] 3 tests from MrcSerializer (6 ms total)
51:
51: [----------] 4 tests from MrcDensityMap
51: [ RUN ] MrcDensityMap.RoundTripIsIdempotent
51: [ OK ] MrcDensityMap.RoundTripIsIdempotent (5 ms)
51: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent
51: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms)
51: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile
51: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (1 ms)
51: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile
51: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (7 ms)
51: [----------] 4 tests from MrcDensityMap (15 ms total)
51:
51: [----------] 8 tests from MrcDensityMapHeaderTest
51: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader
51: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect
51: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid
51: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (1 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (1 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.IsSane
51: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms)
51: [----------] 8 tests from MrcDensityMapHeaderTest (2 ms total)
51:
51: [----------] 10 tests from ReadTest
51: [ RUN ] ReadTest.get_eint_ReadsInteger
51: [ OK ] ReadTest.get_eint_ReadsInteger (1 ms)
51: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side '0.8' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms)
51: [ RUN ] ReadTest.get_eint_WarnsAboutString
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side 'hello' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
51: [ RUN ] ReadTest.get_eint64_ReadsInteger
51: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
51: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side '0.8' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (1 ms)
51: [ RUN ] ReadTest.get_eint64_WarnsAboutString
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side 'hello' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
51: [ RUN ] ReadTest.get_ereal_ReadsInteger
51: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
51: [ RUN ] ReadTest.get_ereal_ReadsFloat
51: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
51: [ RUN ] ReadTest.get_ereal_WarnsAboutString
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side 'hello' for parameter 'test' in parameter file is not a
51: real value
51:
51:
51: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
51: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString
51: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms)
51: [----------] 10 tests from ReadTest (5 ms total)
51:
51: [----------] 1 test from FileIOXdrSerializerTest
51: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect
51: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (1 ms)
51: [----------] 1 test from FileIOXdrSerializerTest (1 ms total)
51:
51: [----------] 2 tests from TngTest
51: [ RUN ] TngTest.CanOpenTngFile
51: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
51: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
51: [ OK ] TngTest.CanOpenTngFile (0 ms)
51: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
51: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (1 ms)
51: [----------] 2 tests from TngTest (2 ms total)
51:
51: [----------] 4 tests from XvgioTest
51: [ RUN ] XvgioTest.readXvgIntWorks
51: [ OK ] XvgioTest.readXvgIntWorks (1 ms)
51: [ RUN ] XvgioTest.readXvgRealWorks
51: [ OK ] XvgioTest.readXvgRealWorks (1 ms)
51: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks
51: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (2 ms)
51: [ RUN ] XvgioTest.readXvgDeprecatedWorks
51: [ OK ] XvgioTest.readXvgDeprecatedWorks (1 ms)
51: [----------] 4 tests from XvgioTest (5 ms total)
51:
51: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (3 ms)
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (3 ms)
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (9 ms)
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (3 ms)
51: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (18 ms total)
51:
51: [----------] Global test environment tear-down
51: [==========] 42 tests from 10 test cases ran. (66 ms total)
51: [ PASSED ] 42 tests.
51/65 Test #51: FileIOTests ........................... Passed 0.14 sec
test 52
Start 52: SelectionUnitTests
52: Test command: /<<PKGBUILDDIR>>/build/basic/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SelectionUnitTests.xml"
52: Test timeout computed to be: 30
52: [==========] Running 192 tests from 11 test cases.
52: [----------] Global test environment set-up.
52: [----------] 1 test from IndexGroupTest
52: [ RUN ] IndexGroupTest.RemovesDuplicates
52: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
52: [----------] 1 test from IndexGroupTest (0 ms total)
52:
52: [----------] 15 tests from IndexBlockTest
52: [ RUN ] IndexBlockTest.CreatesUnknownBlock
52: [ OK ] IndexBlockTest.CreatesUnknownBlock (42 ms)
52: [ RUN ] IndexBlockTest.CreatesAtomBlock
52: [ OK ] IndexBlockTest.CreatesAtomBlock (1 ms)
52: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology
52: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (2 ms)
52: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology
52: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (26 ms)
52: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology
52: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (1 ms)
52: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology
52: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (2 ms)
52: [ RUN ] IndexBlockTest.CreatesSingleBlock
52: [ OK ] IndexBlockTest.CreatesSingleBlock (1 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
52: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
52: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
52: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (1 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms)
52: [----------] 15 tests from IndexBlockTest (79 ms total)
52:
52: [----------] 11 tests from IndexMapTest
52: [ RUN ] IndexMapTest.InitializesAtomBlock
52: [ OK ] IndexMapTest.InitializesAtomBlock (1 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
52: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (1 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
52: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (2 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
52: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (2 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
52: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (1 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
52: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (2 ms)
52: [ RUN ] IndexMapTest.InitializesMoleculeBlock
52: [ OK ] IndexMapTest.InitializesMoleculeBlock (1 ms)
52: [ RUN ] IndexMapTest.MapsSingleBlock
52: [ OK ] IndexMapTest.MapsSingleBlock (1 ms)
52: [ RUN ] IndexMapTest.MapsResidueBlocks
52: [ OK ] IndexMapTest.MapsResidueBlocks (3 ms)
52: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
52: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (2 ms)
52: [ RUN ] IndexMapTest.HandlesMultipleRequests
52: [ OK ] IndexMapTest.HandlesMultipleRequests (40 ms)
52: [----------] 11 tests from IndexMapTest (57 ms total)
52:
52: [----------] 3 tests from IndexGroupsAndNamesTest
52: [ RUN ] IndexGroupsAndNamesTest.containsNames
52: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms)
52: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing
52: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (1 ms)
52: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect
52: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms)
52: [----------] 3 tests from IndexGroupsAndNamesTest (1 ms total)
52:
52: [----------] 15 tests from NeighborhoodSearchTest
52: [ RUN ] NeighborhoodSearchTest.SimpleSearch
52: [ OK ] NeighborhoodSearchTest.SimpleSearch (67 ms)
52: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
52: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (68 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchBox
52: [ OK ] NeighborhoodSearchTest.GridSearchBox (12 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
52: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (43 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
52: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (22 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
52: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (12 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
52: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (12 ms)
52: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
52: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
52: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (260 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
52: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (1 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
52: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (1 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
52: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
52: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms)
52: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
52: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (25 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
52: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (10 ms)
52: [----------] 15 tests from NeighborhoodSearchTest (536 ms total)
52:
52: [----------] 12 tests from PositionCalculationTest
52: [ RUN ] PositionCalculationTest.ComputesAtomPositions
52: [ OK ] PositionCalculationTest.ComputesAtomPositions (6 ms)
52: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
52: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (2 ms)
52: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
52: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (38 ms)
52: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
52: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (2 ms)
52: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
52: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (2 ms)
52: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
52: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (2 ms)
52: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
52: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (2 ms)
52: [ RUN ] PositionCalculationTest.ComputesPositionMask
52: [ OK ] PositionCalculationTest.ComputesPositionMask (12 ms)
52: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
52: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (1 ms)
52: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
52: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (2 ms)
52: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
52: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (2 ms)
52: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
52: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (2 ms)
52: [----------] 12 tests from PositionCalculationTest (84 ms total)
52:
52: [----------] 29 tests from SelectionCollectionTest
52: [ RUN ] SelectionCollectionTest.HandlesNoSelections
52: [ OK ] SelectionCollectionTest.HandlesNoSelections (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
52: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (21 ms)
52: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
52: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
52: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (2 ms)
52: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
52: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
52: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
52: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (3 ms)
52: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
52: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
52: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
52: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
52: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
52: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
52: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
52: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
52: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
52: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (2 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
52: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (2 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
52: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (2 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
52: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (2 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
52: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
52: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (2 ms)
52: [----------] 29 tests from SelectionCollectionTest (83 ms total)
52:
52: [----------] 14 tests from SelectionCollectionInteractiveTest
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
52: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
52: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
52: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
52: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (4 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
52: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
52: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
52: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
52: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (4 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
52: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
52: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (2 ms)
52: [----------] 14 tests from SelectionCollectionInteractiveTest (48 ms total)
52:
52: [----------] 66 tests from SelectionCollectionDataTest
52: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
52: [ OK ] SelectionCollectionDataTest.HandlesAllNone (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
52: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesResnr
52: [ OK ] SelectionCollectionDataTest.HandlesResnr (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
52: [ OK ] SelectionCollectionDataTest.HandlesResIndex (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
52: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
52: [ OK ] SelectionCollectionDataTest.HandlesAtomname (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
52: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
52: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesChain
52: [ OK ] SelectionCollectionDataTest.HandlesChain (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMass
52: [ OK ] SelectionCollectionDataTest.HandlesMass (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesCharge
52: [ OK ] SelectionCollectionDataTest.HandlesCharge (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
52: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
52: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
52: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBeta
52: [ OK ] SelectionCollectionDataTest.HandlesBeta (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesResname
52: [ OK ] SelectionCollectionDataTest.HandlesResname (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
52: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (7 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
52: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
52: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
52: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (9 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (16 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (27 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
52: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (25 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
52: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (11 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
52: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (12 ms)
52: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
52: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (9 ms)
52: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
52: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
52: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
52: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
52: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
52: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
52: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (8 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
52: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
52: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
52: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
52: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
52: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
52: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
52: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
52: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
52: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
52: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
52: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
52: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
52: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
52: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
52: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
52: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
52: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
52: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (8 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
52: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (7 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
52: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
52: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (7 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
52: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (7 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
52: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
52: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
52: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
52: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
52: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
52: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
52: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
52: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
52: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
52: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (4 ms)
52: [----------] 66 tests from SelectionCollectionDataTest (400 ms total)
52:
52: [----------] 17 tests from SelectionOptionTest
52: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
52: [ OK ] SelectionOptionTest.ParsesSimpleSelection (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
52: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
52: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (2 ms)
52: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
52: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (3 ms)
52: [ RUN ] SelectionOptionTest.ChecksEmptySelections
52: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms)
52: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
52: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooManySelections
52: [ OK ] SelectionOptionTest.HandlesTooManySelections (2 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
52: [ OK ] SelectionOptionTest.HandlesTooFewSelections (2 ms)
52: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
52: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesAdjuster
52: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (2 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (2 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
52: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
52: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
52: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (2 ms)
52: [----------] 17 tests from SelectionOptionTest (31 ms total)
52:
52: [----------] 9 tests from SelectionFileOptionTest
52: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
52: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (2 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
52: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (2 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
52: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (2 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
52: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (2 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
52: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (2 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
52: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (2 ms)
52: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
52: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
52: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (2 ms)
52: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
52: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (2 ms)
52: [----------] 9 tests from SelectionFileOptionTest (17 ms total)
52:
52: [----------] Global test environment tear-down
52: [==========] 192 tests from 11 test cases ran. (1341 ms total)
52: [ PASSED ] 192 tests.
52/65 Test #52: SelectionUnitTests .................... Passed 1.43 sec
test 53
Start 53: MdrunOutputTests
53: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunOutputTests.xml"
53: Test timeout computed to be: 600
53: [==========] Running 12 tests from 5 test cases.
53: [----------] Global test environment set-up.
53: [----------] 1 test from MdrunTest
53: [ RUN ] MdrunTest.WritesHelp
53: [ OK ] MdrunTest.WritesHelp (101 ms)
53: [----------] 1 test from MdrunTest (101 ms total)
53:
53: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
53: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
53: Generating 1-4 interactions: fudge = 0.5
53: Number of degrees of freedom in T-Coupling group rest is 9.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
53: NVE simulation: will use the initial temperature of 2573.591 K for
53: determining the Verlet buffer size
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc2'
53: 1 steps, 0.0 ps.
53: Setting the LD random seed to 935310879
53:
53: Generated 3 of the 3 non-bonded parameter combinations
53:
53: Generated 3 of the 3 1-4 parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.338 0.169 199.7
53: (ns/day) (hour/ns)
53: Performance: 1.022 23.487
53:
Reading frame 0 time 0.000
53: # Atoms 6
53:
Reading frame 1 time 0.001
Last frame 1 time 0.001
53:
53:
53: Item #frames Timestep (ps)
53: Step 2 0.001
53: Time 2 0.001
53: Lambda 0
53: Coords 2 0.001
53: Velocities 0
53: Forces 0
53: Box 2 0.001
53: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
53: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (228 ms)
53: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
53: Generating 1-4 interactions: fudge = 0.5
53: Number of degrees of freedom in T-Coupling group rest is 9.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
53: NVE simulation: will use the initial temperature of 2573.591 K for
53: determining the Verlet buffer size
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc2'
53: 1 steps, 0.0 ps.
53: Setting the LD random seed to -137379849
53:
53: Generated 3 of the 3 non-bonded parameter combinations
53:
53: Generated 3 of the 3 1-4 parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.341 0.171 199.7
53: (ns/day) (hour/ns)
53: Performance: 1.012 23.704
53:
Reading frame 0 time 0.000
53: # Atoms 6
53:
Reading frame 1 time 0.001
Last frame 1 time 0.001
53:
53:
53: Item #frames Timestep (ps)
53: Step 2 0.001
53: Time 2 0.001
53: Lambda 0
53: Coords 2 0.001
53: Velocities 0
53: Forces 0
53: Box 2 0.001
53: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
53: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (210 ms)
53: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
53: Generating 1-4 interactions: fudge = 0.5
53: Number of degrees of freedom in T-Coupling group rest is 9.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
53: NVE simulation: will use the initial temperature of 2573.591 K for
53: determining the Verlet buffer size
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc2'
53: 1 steps, 0.0 ps.
53: Setting the LD random seed to -76551177
53:
53: Generated 3 of the 3 non-bonded parameter combinations
53:
53: Generated 3 of the 3 1-4 parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.342 0.171 199.7
53: (ns/day) (hour/ns)
53: Performance: 1.008 23.807
53:
Reading frame 0 time 0.000
53: # Atoms 3
53:
Reading frame 1 time 0.001
Last frame 1 time 0.001
53:
53:
53: Item #frames Timestep (ps)
53: Step 2 0.001
53: Time 2 0.001
53: Lambda 0
53: Coords 2 0.001
53: Velocities 0
53: Forces 0
53: Box 2 0.001
53: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
53: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (211 ms)
53: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (650 ms total)
53:
53: [----------] 2 tests from Argon12/OutputFiles
53: [ RUN ] Argon12/OutputFiles.FilesArePresent/0
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
53: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
53: that with the Verlet scheme, nstlist has no effect on the accuracy of
53: your simulation.
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
53: Setting nstcalcenergy (100) equal to nstenergy (4)
53:
53: Number of degrees of freedom in T-Coupling group System is 33.00
53:
53: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
53: NVE simulation: will use the initial temperature of 68.810 K for
53: determining the Verlet buffer size
53:
53:
53: There were 3 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'Argon'
53: 16 steps, 0.0 ps.
53: Generated 1 of the 1 non-bonded parameter combinations
53:
53: Excluding 1 bonded neighbours molecule type 'Argon'
53:
53: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
53:
53: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.388 0.194 199.7
53: (ns/day) (hour/ns)
53: Performance: 7.558 3.176
53: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (251 ms)
53: [ RUN ] Argon12/OutputFiles.FilesArePresent/1
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
53: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
53: that with the Verlet scheme, nstlist has no effect on the accuracy of
53: your simulation.
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
53: Setting nstcalcenergy (100) equal to nstenergy (4)
53:
53: Number of degrees of freedom in T-Coupling group System is 33.00
53:
53: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
53: NVE simulation: will use the initial temperature of 68.810 K for
53: determining the Verlet buffer size
53:
53:
53: There were 3 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'Argon'
53: 16 steps, 0.0 ps.
53: Generated 1 of the 1 non-bonded parameter combinations
53:
53: Excluding 1 bonded neighbours molecule type 'Argon'
53:
53: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
53:
53: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.413 0.207 199.9
53: (ns/day) (hour/ns)
53: Performance: 7.099 3.381
53: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (244 ms)
53: [----------] 2 tests from Argon12/OutputFiles (496 ms total)
53:
53: [----------] 3 tests from MdrunCanWrite/Trajectories
53: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 6 steps, 0.0 ps.
53: Setting the LD random seed to -1380205129
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.286 0.143 199.5
53: (ns/day) (hour/ns)
53: Performance: 4.218 5.690
53: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (188 ms)
53: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 6 steps, 0.0 ps.
53: Setting the LD random seed to -338710609
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.331 0.166 199.5
53: (ns/day) (hour/ns)
53: Performance: 3.641 6.592
53: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (211 ms)
53: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 6 steps, 0.0 ps.
53: Setting the LD random seed to 2120146671
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.317 0.159 199.5
53: (ns/day) (hour/ns)
53: Performance: 3.812 6.297
53: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (201 ms)
53: [----------] 3 tests from MdrunCanWrite/Trajectories (600 ms total)
53:
53: [----------] 3 tests from MdrunCanWrite/NptTrajectories
53: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 2 steps, 0.0 ps.
53: Setting the LD random seed to -524686
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.262 0.132 199.4
53: (ns/day) (hour/ns)
53: Performance: 1.970 12.185
53: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (173 ms)
53: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 2 steps, 0.0 ps.
53: Setting the LD random seed to -1086358594
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.294 0.148 199.5
53: (ns/day) (hour/ns)
53: Performance: 1.756 13.669
53: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (188 ms)
53: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 2 steps, 0.0 ps.
53: Setting the LD random seed to -8388611
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.294 0.147 199.5
53: (ns/day) (hour/ns)
53: Performance: 1.759 13.644
53: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (188 ms)
53: [----------] 3 tests from MdrunCanWrite/NptTrajectories (552 ms total)
53:
53: [----------] Global test environment tear-down
53: [==========] 12 tests from 5 test cases ran. (2542 ms total)
53: [ PASSED ] 12 tests.
53/65 Test #53: MdrunOutputTests ...................... Passed 2.61 sec
test 54
Start 54: MdrunModulesTests
54: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunModulesTests.xml"
54: Test timeout computed to be: 600
54: [==========] Running 15 tests from 3 test cases.
54: [----------] Global test environment set-up.
54: [----------] 9 tests from DensityFittingTest
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -3.8565400e+03
54: Maximum force = 2.8846870e+03 on atom 3
54: Norm of force = 1.0754448e+03
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to 934002663
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (44 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -9.8208447e+03
54: Maximum force = 4.7331094e+03 on atom 2
54: Norm of force = 1.7801224e+03
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to 1542250171
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (38 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff
54:
54: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1050:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out.
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (33 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -9.7604385e+03
54: Maximum force = 4.6344800e+03 on atom 2
54: Norm of force = 1.7575605e+03
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to -172233745
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (38 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff
54:
54: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1050:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out.
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (32 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -3.8565400e+03
54: Maximum force = 2.8846870e+03 on atom 3
54: Norm of force = 1.0754448e+03
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to 2146958821
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (38 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -2.7138666e+04
54: Maximum force = 4.3409717e+03 on atom 2
54: Norm of force = 1.2549793e+03
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to -1692545307
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (41 ms)
54: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch
54:
54: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1050:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out.
54: Setting the LD random seed to -20546
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (38 ms)
54: [ RUN ] DensityFittingTest.CheckpointWorks
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
54: Setting nstcalcenergy (100) equal to nstenergy (2)
54:
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
54: NVE simulation: will use the initial temperature of 68.810 K for
54: determining the Verlet buffer size
54:
54:
54: There were 2 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting mdrun 'Argon'
54: 2 steps, 0.0 ps.
54: Setting the LD random seed to -1130753
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K
54:
54: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
54:
54: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
54:
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54:
54: This run will generate roughly 0 Mb of data
54:
54: Writing final coordinates.
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.278 0.139 199.6
54: (ns/day) (hour/ns)
54: Performance: 1.863 12.885
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
54: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps
54: Can not increase nstlist because an NVE ensemble is used
54:
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting mdrun 'Argon'
54: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps).
54:
54: Writing final coordinates.
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.288 0.144 199.6
54: (ns/day) (hour/ns)
54: Performance: 2.995 8.014
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (332 ms)
54: [----------] 9 tests from DensityFittingTest (635 ms total)
54:
54: [----------] 4 tests from MimicTest
54: [ RUN ] MimicTest.OneQuantumMol
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 21.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
54: NVE simulation with an initial temperature of zero: will use a Verlet
54: buffer of 10%. Check your energy drift!
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
54:
54: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.004 0.002 190.2
54: (ns/day) (hour/ns)
54: Performance: 40.445 0.593
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -676677763
54:
54: Generated 10 of the 10 non-bonded parameter combinations
54:
54: Generated 10 of the 10 1-4 parameter combinations
54:
54: Excluding 2 bonded neighbours molecule type 'SOL'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.OneQuantumMol (64 ms)
54: [ RUN ] MimicTest.AllQuantumMol
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 21.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
54: NVE simulation with an initial temperature of zero: will use a Verlet
54: buffer of 10%. Check your energy drift!
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
54:
54: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.003 0.001 183.7
54: (ns/day) (hour/ns)
54: Performance: 62.341 0.385
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 264100847
54:
54: Generated 10 of the 10 non-bonded parameter combinations
54:
54: Generated 10 of the 10 1-4 parameter combinations
54:
54: Excluding 2 bonded neighbours molecule type 'SOL'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.AllQuantumMol (38 ms)
54: [ RUN ] MimicTest.TwoQuantumMol
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 21.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
54: NVE simulation with an initial temperature of zero: will use a Verlet
54: buffer of 10%. Check your energy drift!
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
54:
54: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.003 0.001 176.4
54: (ns/day) (hour/ns)
54: Performance: 60.097 0.399
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -1074989958
54:
54: Generated 10 of the 10 non-bonded parameter combinations
54:
54: Generated 10 of the 10 1-4 parameter combinations
54:
54: Excluding 2 bonded neighbours molecule type 'SOL'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.TwoQuantumMol (36 ms)
54: [ RUN ] MimicTest.BondCuts
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 66.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
54: NVE simulation: will use the initial temperature of 300.368 K for
54: determining the Verlet buffer size
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
54:
54: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.004 0.002 190.6
54: (ns/day) (hour/ns)
54: Performance: 39.000 0.615
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -139550721
54:
54: Generated 2211 of the 2211 non-bonded parameter combinations
54:
54: Generated 2211 of the 2211 1-4 parameter combinations
54:
54: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
54:
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
54:
54: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
54:
54: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
54:
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.BondCuts (145 ms)
54: [----------] 4 tests from MimicTest (283 ms total)
54:
54: [----------] 2 tests from WithIntegrator/ImdTest
54: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0
54: Generating 1-4 interactions: fudge = 1
54:
54: NOTE 1 [file glycine_vacuo.top, line 12]:
54: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an
54: estimated oscillational period of 1.0e-02 ps, which is less than 10 times
54: the time step of 2.0e-03 ps.
54: Maybe you forgot to change the constraints mdp option.
54:
54: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
54: Number of degrees of freedom in T-Coupling group System is 27.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
54: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34
54:
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: IMD: Enabled. This simulation will accept incoming IMD connections.
54: IMD: Pulling from IMD remote is enabled (-imdpull).
54: IMD: Setting port for connection requests to 0.
54: IMD: Setting up incoming socket.
54: IMD: Listening for IMD connection on port 42691.
54: IMD: -imdwait not set, starting simulation.
54: starting mdrun 'Glycine'
54: 2 steps, 0.0 ps.
54: Setting the LD random seed to -1746960972
54:
54: Generated 20503 of the 20503 non-bonded parameter combinations
54:
54: Generated 17396 of the 20503 1-4 parameter combinations
54:
54: Excluding 3 bonded neighbours molecule type 'Glycine'
54:
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
54:
54: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
54:
54: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm
54:
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54:
54: This run will generate roughly 0 Mb of data
54:
54: Writing final coordinates.
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.369 0.185 199.6
54: (ns/day) (hour/ns)
54: Performance: 2.803 8.562
54: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (1334 ms)
54: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
54: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not
54: apply to steep.
54:
54: Generating 1-4 interactions: fudge = 1
54: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
54: Number of degrees of freedom in T-Coupling group System is 27.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: IMD: Enabled. This simulation will accept incoming IMD connections.
54: IMD: Pulling from IMD remote is enabled (-imdpull).
54: IMD: Setting port for connection requests to 0.
54: IMD: Setting up incoming socket.
54: IMD: Listening for IMD connection on port 42073.
54: IMD: -imdwait not set, starting simulation.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = 1.1977063e+03
54: Maximum force = 1.7794877e+04 on atom 9
54: Norm of force = 7.8732901e+03
54: Setting the LD random seed to -65609
54:
54: Generated 20503 of the 20503 non-bonded parameter combinations
54:
54: Generated 17396 of the 20503 1-4 parameter combinations
54:
54: Excluding 3 bonded neighbours molecule type 'Glycine'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (997 ms)
54: [----------] 2 tests from WithIntegrator/ImdTest (2332 ms total)
54:
54: [----------] Global test environment tear-down
54: [==========] 15 tests from 3 test cases ran. (3364 ms total)
54: [ PASSED ] 15 tests.
54/65 Test #54: MdrunModulesTests ..................... Passed 3.43 sec
test 55
Start 55: MdrunIOTests
55: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunIOTests.xml"
55: Test timeout computed to be: 600
55: [==========] Running 61 tests from 10 test cases.
55: [----------] Global test environment set-up.
55: [----------] 3 tests from GromppTest
55: [ RUN ] GromppTest.EmptyMdpFileWorks
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
55: For a correct single-point energy evaluation with nsteps = 0, use
55: continuation = yes to avoid constraining the input coordinates.
55:
55: Number of degrees of freedom in T-Coupling group rest is 12.00
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
55: NVE simulation: will use the initial temperature of 1046.791 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Setting the LD random seed to -268632131
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: [ OK ] GromppTest.EmptyMdpFileWorks (28 ms)
55: [ RUN ] GromppTest.SimulatedAnnealingWorks
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
55: For a correct single-point energy evaluation with nsteps = 0, use
55: continuation = yes to avoid constraining the input coordinates.
55:
55: Simulated annealing for group rest: Periodic, 4 timepoints
55: Time (ps) Temperature (K)
55: 0.0 298.0
55: 2.0 320.0
55: 4.0 320.0
55: 6.0 298.0
55: Number of degrees of freedom in T-Coupling group rest is 12.00
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
55: NVE simulation: will use the initial temperature of 1046.791 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Setting the LD random seed to -145248300
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: [ OK ] GromppTest.SimulatedAnnealingWorks (24 ms)
55: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
55: For a correct single-point energy evaluation with nsteps = 0, use
55: continuation = yes to avoid constraining the input coordinates.
55:
55: Simulated annealing for group Methanol: Single, 3 timepoints
55: Time (ps) Temperature (K)
55: 0.0 298.0
55: 3.0 280.0
55: 6.0- 270.0
55: Simulated annealing for group SOL: Periodic, 4 timepoints
55: Time (ps) Temperature (K)
55: 0.0 298.0
55: 2.0 320.0
55: 4.0 320.0
55: 6.0 298.0
55: Number of degrees of freedom in T-Coupling group Methanol is 7.20
55: Number of degrees of freedom in T-Coupling group SOL is 4.80
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
55: NVE simulation: will use the initial temperature of 1046.791 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Setting the LD random seed to 132104168
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (24 ms)
55: [----------] 3 tests from GromppTest (78 ms total)
55:
55: [----------] 6 tests from MdrunTerminationTest
55: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to 1741684703
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.302 0.151 199.6
55: (ns/day) (hour/ns)
55: Performance: 1.716 13.984
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.268 0.134 199.6
55: (ns/day) (hour/ns)
55: Performance: 1.932 12.420
55: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (343 ms)
55: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 10 to 1, rlist from 1.024 to 1
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 100 steps, 0.1 ps.
55:
55: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps
55: Setting the LD random seed to -1610613004
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.262 0.131 199.5
55: (ns/day) (hour/ns)
55: Performance: 1.977 12.139
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Setting nsteps to 102
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 102 steps, 0.1 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 100
55: Runtime for the run 0.1 ps
55: Run end step 100
55: Run end time 0.1 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 102
55: Runtime for the run 0.102 ps
55: Run end step 102
55: Run end time 0.102 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.276 0.138 199.6
55: (ns/day) (hour/ns)
55: Performance: 63.089 0.380
55: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (322 ms)
55: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -621119489
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.262 0.131 199.6
55: (ns/day) (hour/ns)
55: Performance: 1.978 12.133
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.315 0.158 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.645 14.587
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Setting nsteps to 6
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 6
55: Runtime for the run 0.006 ps
55: Run end step 6
55: Run end time 0.006 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.293 0.147 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.767 13.580
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Setting nsteps to 8
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 6
55: Runtime for the run 0.006 ps
55: Run end step 6
55: Run end time 0.006 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 8
55: Runtime for the run 0.008 ps
55: Run end step 8
55: Run end time 0.008 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.285 0.143 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.815 13.225
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.001 0.001 162.6
55: (ns/day) (hour/ns)
55: Performance: 111.094 0.216
55: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (693 ms)
55: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -562074145
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.297 0.149 199.6
55: (ns/day) (hour/ns)
55: Performance: 1.743 13.768
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps.
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.327 0.164 199.5
55: (ns/day) (hour/ns)
55: Performance: 2.635 9.108
55: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (362 ms)
55: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -470818819
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.305 0.153 199.6
55: (ns/day) (hour/ns)
55: Performance: 1.696 14.153
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Setting nsteps to 4
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (192 ms)
55: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -53485571
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.298 0.149 199.6
55: (ns/day) (hour/ns)
55: Performance: 1.736 13.821
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.284 0.142 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.826 13.145
55: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (341 ms)
55: [----------] 6 tests from MdrunTerminationTest (2254 ms total)
55:
55: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks
55: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.398 0.199 199.7
55: (ns/day) (hour/ns)
55: Performance: 7.364 3.259
55: trr version: GMX_trn_file (single precision)
55:
55:
55: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (252 ms)
55: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.365 0.183 199.8
55: (ns/day) (hour/ns)
55: Performance: 8.042 2.984
55:
55:
55: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (223 ms)
55: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (475 ms total)
55:
55: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.382 0.191 199.7
55: (ns/day) (hour/ns)
55: Performance: 7.673 3.128
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.352 0.176 199.4
55: (ns/day) (hour/ns)
55: Performance: 4.406 5.447
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.329 0.165 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.715 5.090
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (624 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.381 0.191 199.8
55: (ns/day) (hour/ns)
55: Performance: 7.695 3.119
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.349 0.175 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.447 5.397
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.322 0.161 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.821 4.979
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (631 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.499 0.250 199.8
55: (ns/day) (hour/ns)
55: Performance: 5.877 4.084
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.424 0.212 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.665 6.549
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.355 0.178 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.369 5.493
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (722 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.434 0.217 199.8
55: (ns/day) (hour/ns)
55: Performance: 6.765 3.548
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.360 0.180 199.6
55: (ns/day) (hour/ns)
55: Performance: 4.317 5.560
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.352 0.176 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.407 5.446
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (655 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.342 0.171 199.7
55: (ns/day) (hour/ns)
55: Performance: 8.579 2.797
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.335 0.168 199.5
55: (ns/day) (hour/ns)
55: Performance: 4.636 5.177
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.335 0.168 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.636 5.177
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (595 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.330 0.165 199.8
55: (ns/day) (hour/ns)
55: Performance: 8.887 2.701
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.374 0.187 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.158 5.772
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.394 0.197 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.944 6.086
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (649 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.383 0.192 199.7
55: (ns/day) (hour/ns)
55: Performance: 7.669 3.129
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.443 0.222 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.507 6.844
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.375 0.188 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.142 5.795
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (688 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.341 0.171 199.7
55: (ns/day) (hour/ns)
55: Performance: 8.609 2.788
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.357 0.179 199.6
55: (ns/day) (hour/ns)
55: Performance: 4.347 5.521
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.515 0.258 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.015 7.961
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (711 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.426 0.214 199.6
55: (ns/day) (hour/ns)
55: Performance: 6.875 3.491
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.394 0.198 199.3
55: (ns/day) (hour/ns)
55: Performance: 3.936 6.097
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.435 0.218 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.573 6.717
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (914 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.407 0.204 199.6
55: (ns/day) (hour/ns)
55: Performance: 7.207 3.330
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.374 0.188 199.4
55: (ns/day) (hour/ns)
55: Performance: 4.142 5.794
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.418 0.209 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.718 6.455
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (853 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.785 0.393 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.739 6.419
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.405 0.203 199.4
55: (ns/day) (hour/ns)
55: Performance: 3.824 6.275
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.383 0.192 199.6
55: (ns/day) (hour/ns)
55: Performance: 4.057 5.916
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (1247 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.619 0.310 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.739 5.064
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.829 0.415 199.7
55: (ns/day) (hour/ns)
55: Performance: 1.873 12.811
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.537 0.269 199.7
55: (ns/day) (hour/ns)
55: Performance: 2.892 8.298
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (1364 ms)
55: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (9656 ms total)
55:
55: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.013 0.507 199.8
55: (ns/day) (hour/ns)
55: Performance: 2.896 8.286
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.519 0.260 199.3
55: (ns/day) (hour/ns)
55: Performance: 2.986 8.036
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.630 0.315 199.7
55: (ns/day) (hour/ns)
55: Performance: 2.467 9.729
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (1444 ms)
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.602 0.301 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.878 4.920
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.591 0.296 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.628 9.132
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.580 0.290 199.7
55: (ns/day) (hour/ns)
55: Performance: 2.679 8.959
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (1145 ms)
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.480 0.240 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.114 3.925
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.447 0.224 199.2
55: (ns/day) (hour/ns)
55: Performance: 3.464 6.929
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.441 0.221 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.517 6.825
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (1153 ms)
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.507 0.254 199.7
55: (ns/day) (hour/ns)
55: Performance: 5.783 4.150
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.531 0.267 198.8
55: (ns/day) (hour/ns)
55: Performance: 2.910 8.248
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.440 0.220 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.530 6.798
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (1111 ms)
55: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (4854 ms total)
55:
55: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.451 0.226 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.500 3.692
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.346 0.173 199.4
55: (ns/day) (hour/ns)
55: Performance: 4.483 5.353
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.329 0.165 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.720 5.084
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (662 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.382 0.191 199.7
55: (ns/day) (hour/ns)
55: Performance: 7.673 3.128
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.351 0.176 199.5
55: (ns/day) (hour/ns)
55: Performance: 4.425 5.424
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.552 0.276 199.8
55: (ns/day) (hour/ns)
55: Performance: 2.815 8.525
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (734 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.405 0.203 199.7
55: (ns/day) (hour/ns)
55: Performance: 7.242 3.314
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.334 0.167 199.5
55: (ns/day) (hour/ns)
55: Performance: 4.647 5.164
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.333 0.167 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.656 5.155
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (621 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.366 0.183 199.8
55: (ns/day) (hour/ns)
55: Performance: 8.008 2.997
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.334 0.167 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.652 5.159
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.332 0.167 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.670 5.139
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (601 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.385 0.193 199.8
55: (ns/day) (hour/ns)
55: Performance: 7.617 3.151
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.357 0.179 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.353 5.513
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.332 0.166 199.6
55: (ns/day) (hour/ns)
55: Performance: 4.675 5.134
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (623 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.361 0.181 199.7
55: (ns/day) (hour/ns)
55: Performance: 8.132 2.951
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.355 0.178 199.5
55: (ns/day) (hour/ns)
55: Performance: 4.372 5.490
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.329 0.165 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.724 5.081
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (611 ms)
55: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (3852 ms total)
55:
55: [----------] 6 tests from NPH/MdrunNoAppendContinuationIsExact
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.409 0.205 199.7
55: (ns/day) (hour/ns)
55: Performance: 7.177 3.344
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.368 0.185 199.4
55: (ns/day) (hour/ns)
55: Performance: 4.213 5.697
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.338 0.169 199.6
55: (ns/day) (hour/ns)
55: Performance: 4.591 5.228
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (651 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.366 0.183 199.7
55: (ns/day) (hour/ns)
55: Performance: 8.014 2.995
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.334 0.168 199.4
55: (ns/day) (hour/ns)
55: Performance: 4.641 5.171
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.355 0.178 199.6
55: (ns/day) (hour/ns)
55: Performance: 4.370 5.492
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (611 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.365 0.183 199.7
55: (ns/day) (hour/ns)
55: Performance: 8.035 2.987
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.357 0.179 199.4
55: (ns/day) (hour/ns)
55: Performance: 4.346 5.522
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.354 0.178 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.380 5.479
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (622 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.409 0.205 199.7
55: (ns/day) (hour/ns)
55: Performance: 7.164 3.350
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.334 0.168 199.4
55: (ns/day) (hour/ns)
55: Performance: 4.636 5.177
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.333 0.167 199.6
55: (ns/day) (hour/ns)
55: Performance: 4.664 5.146
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (622 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.367 0.184 199.8
55: (ns/day) (hour/ns)
55: Performance: 7.993 3.002
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.221 0.611 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.273 18.849
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.323 0.162 199.6
55: (ns/day) (hour/ns)
55: Performance: 4.802 4.998
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (1048 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.510 0.255 199.8
55: (ns/day) (hour/ns)
55: Performance: 5.753 4.171
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.329 0.665 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.169 20.523
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.461 0.231 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.366 7.131
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (1243 ms)
55: [----------] 6 tests from NPH/MdrunNoAppendContinuationIsExact (4798 ms total)
55:
55: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.458 0.731 199.3
55: (ns/day) (hour/ns)
55: Performance: 2.009 11.948
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.484 0.243 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.203 7.492
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.392 0.196 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.962 6.058
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (1265 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.348 0.174 199.6
55: (ns/day) (hour/ns)
55: Performance: 8.425 2.849
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.344 0.173 199.4
55: (ns/day) (hour/ns)
55: Performance: 4.507 5.325
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.324 0.162 199.6
55: (ns/day) (hour/ns)
55: Performance: 4.797 5.003
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (611 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.557 0.279 199.8
55: (ns/day) (hour/ns)
55: Performance: 5.271 4.553
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.399 0.200 199.5
55: (ns/day) (hour/ns)
55: Performance: 3.888 6.173
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.346 0.173 199.6
55: (ns/day) (hour/ns)
55: Performance: 4.493 5.342
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (766 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.441 0.221 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.656 3.606
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.528 0.265 199.6
55: (ns/day) (hour/ns)
55: Performance: 2.940 8.165
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.518 0.759 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.024 23.430
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (1364 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.513 0.257 199.8
55: (ns/day) (hour/ns)
55: Performance: 5.725 4.192
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.372 0.187 199.5
55: (ns/day) (hour/ns)
55: Performance: 4.164 5.763
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.372 0.186 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.173 5.751
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (723 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.395 0.198 199.7
55: (ns/day) (hour/ns)
55: Performance: 7.434 3.228
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.418 0.210 199.5
55: (ns/day) (hour/ns)
55: Performance: 3.710 6.469
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.483 0.242 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.214 7.467
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (777 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55:
55: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Using Berendsen pressure coupling invalidates the true ensemble for the
55: thermostat
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: There was 1 warning
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55:
55: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Using Berendsen pressure coupling invalidates the true ensemble for the
55: thermostat
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: There was 1 warning
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.353 0.177 199.6
55: (ns/day) (hour/ns)
55: Performance: 8.299 2.892
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.395 0.198 199.5
55: (ns/day) (hour/ns)
55: Performance: 3.926 6.113
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.356 0.178 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.358 5.507
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (648 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.366 0.183 199.7
55: (ns/day) (hour/ns)
55: Performance: 8.010 2.996
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.373 0.187 199.5
55: (ns/day) (hour/ns)
55: Performance: 4.162 5.766
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.350 0.175 199.6
55: (ns/day) (hour/ns)
55: Performance: 4.438 5.408
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (663 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.399 0.200 199.6
55: (ns/day) (hour/ns)
55: Performance: 7.346 3.267
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.328 0.165 199.3
55: (ns/day) (hour/ns)
55: Performance: 4.726 5.078
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.484 0.242 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.212 7.472
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (699 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.459 0.230 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.392 3.755
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.356 0.178 199.4
55: (ns/day) (hour/ns)
55: Performance: 4.361 5.503
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.354 0.177 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.383 5.475
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (697 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.610 0.305 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.810 4.989
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.450 0.225 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.454 6.948
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.455 0.228 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.411 7.036
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (857 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.380 0.190 199.7
55: (ns/day) (hour/ns)
55: Performance: 7.723 3.108
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.332 0.166 199.3
55: (ns/day) (hour/ns)
55: Performance: 4.674 5.135
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.421 0.211 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.689 6.505
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (677 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.453 0.227 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.480 3.704
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.362 0.181 199.4
55: (ns/day) (hour/ns)
55: Performance: 4.288 5.597
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.388 0.195 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.997 6.005
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (693 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.427 0.214 199.8
55: (ns/day) (hour/ns)
55: Performance: 6.866 3.496
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.400 0.200 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.882 6.182
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.580 0.290 199.8
55: (ns/day) (hour/ns)
55: Performance: 2.677 8.965
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (835 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.399 0.200 199.7
55: (ns/day) (hour/ns)
55: Performance: 7.347 3.267
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.342 0.172 199.4
55: (ns/day) (hour/ns)
55: Performance: 4.529 5.299
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.795 0.398 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.954 12.281
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (883 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15
55: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (0 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16
55: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (1 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.069 0.535 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.745 8.743
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.361 0.181 199.4
55: (ns/day) (hour/ns)
55: Performance: 4.292 5.592
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.379 0.190 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.098 5.856
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (999 ms)
55: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact (13163 ms total)
55:
55: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact
55: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.447 0.224 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.557 3.660
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.355 0.178 199.5
55: (ns/day) (hour/ns)
55: Performance: 4.370 5.491
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.353 0.177 199.6
55: (ns/day) (hour/ns)
55: Performance: 4.394 5.462
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (668 ms)
55: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (668 ms total)
55:
55: [----------] 3 tests from Checking/InitialConstraintsTest
55: [ RUN ] Checking/InitialConstraintsTest.Works/0
55: Number of degrees of freedom in T-Coupling group rest is 11.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 1141.954 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc-and-methanol'
55: 1 steps, 0.0 ps.
55: Setting the LD random seed to -69468166
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.292 0.146 199.5
55: (ns/day) (hour/ns)
55: Performance: 1.183 20.289
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (182 ms)
55: [ RUN ] Checking/InitialConstraintsTest.Works/1
55: Number of degrees of freedom in T-Coupling group rest is 11.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 1141.954 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc-and-methanol'
55: 1 steps, 0.0 ps.
55: Setting the LD random seed to -277874203
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.286 0.143 199.7
55: (ns/day) (hour/ns)
55: Performance: 1.209 19.858
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (179 ms)
55: [ RUN ] Checking/InitialConstraintsTest.Works/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
55: Integrator method md-vv-avek is implemented primarily for validation
55: purposes; for molecular dynamics, you should probably be using md or md-vv
55:
55: Number of degrees of freedom in T-Coupling group rest is 11.00
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
55: NVE simulation: will use the initial temperature of 1141.954 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc-and-methanol'
55: 1 steps, 0.0 ps.
55: Setting the LD random seed to -549589266
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.402 0.201 199.6
55: (ns/day) (hour/ns)
55: Performance: 0.859 27.954
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (274 ms)
55: [----------] 3 tests from Checking/InitialConstraintsTest (635 ms total)
55:
55: [----------] Global test environment tear-down
55: [==========] 61 tests from 10 test cases ran. (40823 ms total)
55: [ PASSED ] 61 tests.
55/65 Test #55: MdrunIOTests .......................... Passed 40.92 sec
test 56
Start 56: MdrunTests
56: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunTests.xml"
56: Test timeout computed to be: 600
56: [==========] Running 14 tests from 6 test cases.
56: [----------] Global test environment set-up.
56: [----------] 1 test from OriresTest
56: [ RUN ] OriresTest.OriresCanRun
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
56: The Berendsen thermostat does not generate the correct kinetic energy
56: distribution. You might want to consider using the V-rescale thermostat.
56:
56: Generating 1-4 interactions: fudge = 0.5
56: Number of degrees of freedom in T-Coupling group System is 518.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
56: You are using a plain Coulomb cut-off, which might produce artifacts.
56: You might want to consider using PME electrostatics.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
56: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank.
56: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164
56:
56:
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1'
56: 10 steps, 0.0 ps.
56: Setting the LD random seed to -5277215
56:
56: Generated 2145 of the 2145 non-bonded parameter combinations
56:
56: Generated 2145 of the 2145 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning H bonds into constraints...
56:
56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
56:
56: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm
56:
56: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm
56:
56: Note that mdrun will redetermine rlist based on the actual pair-list setup
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.477 0.239 199.7
56: (ns/day) (hour/ns)
56: Performance: 7.963 3.014
56: [ OK ] OriresTest.OriresCanRun (2905 ms)
56: [----------] 1 test from OriresTest (2905 ms total)
56:
56: [----------] 1 test from CompelTest
56: [ RUN ] CompelTest.SwapCanRun
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
56: The Berendsen thermostat does not generate the correct kinetic energy
56: distribution. You might want to consider using the V-rescale thermostat.
56:
56: Generating 1-4 interactions: fudge = 0.5
56: Split0 group 'Ch0' contains 83 atoms.
56: Split1 group 'Ch1' contains 83 atoms.
56: Solvent group 'SOL' contains 11931 atoms.
56: Swap group 'NA+' contains 19 atoms.
56: Swap group 'CL-' contains 19 atoms.
56: Number of degrees of freedom in T-Coupling group System is 27869.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
56: You are using a plain Coulomb cut-off, which might produce artifacts.
56: You might want to consider using PME electrostatics.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: SWAP: Determining initial numbers of ions per compartment.
56: SWAP: Setting pointers for checkpoint writing
56: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
56: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
56: starting mdrun 'Channel_coco in octane membrane'
56: 2 steps, 0.0 ps.
56: Setting the LD random seed to -603979841
56:
56: Generated 330891 of the 330891 non-bonded parameter combinations
56:
56: Generated 330891 of the 330891 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein'
56:
56: turning all bonds into constraints...
56:
56: Excluding 3 bonded neighbours molecule type 'OCT'
56:
56: turning all bonds into constraints...
56:
56: Excluding 1 bonded neighbours molecule type 'NA'
56:
56: turning all bonds into constraints...
56:
56: Excluding 1 bonded neighbours molecule type 'CL'
56:
56: turning all bonds into constraints...
56:
56: Excluding 3 bonded neighbours molecule type 'Protein'
56:
56: Excluding 3 bonded neighbours molecule type 'OCT'
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning all bonds into constraints...
56:
56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
56:
56: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
56:
56: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
56:
56: Note that mdrun will redetermine rlist based on the actual pair-list setup
56:
56: This run will generate roughly 1 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 5.769 2.885 200.0
56: (ns/day) (hour/ns)
56: Performance: 0.449 53.429
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
56: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
56:
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: SWAP: Setting pointers for checkpoint writing
56: SWAP: Copying channel fluxes from checkpoint file data
56: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
56: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
56: starting mdrun 'Channel_coco in octane membrane'
56: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 4.953 2.477 200.0
56: (ns/day) (hour/ns)
56: Performance: 0.523 45.871
56: [ OK ] CompelTest.SwapCanRun (10051 ms)
56: [----------] 1 test from CompelTest (10051 ms total)
56:
56: [----------] 6 tests from BondedInteractionsTest
56: [ RUN ] BondedInteractionsTest.NormalBondWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 2 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 183.9
56: (ns/day) (hour/ns)
56: Performance: 72.174 0.333
56: Setting the LD random seed to -536900161
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.NormalBondWorks (34 ms)
56: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 2 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 183.9
56: (ns/day) (hour/ns)
56: Performance: 71.618 0.335
56: Setting the LD random seed to -1078329865
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.TabulatedBondWorks (53 ms)
56: [ RUN ] BondedInteractionsTest.NormalAngleWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 184.0
56: (ns/day) (hour/ns)
56: Performance: 71.959 0.334
56: Setting the LD random seed to -436473897
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.NormalAngleWorks (32 ms)
56: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.006 0.003 193.6
56: (ns/day) (hour/ns)
56: Performance: 27.111 0.885
56: Setting the LD random seed to -654852178
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (41 ms)
56: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.003 0.002 187.2
56: (ns/day) (hour/ns)
56: Performance: 49.291 0.487
56: Setting the LD random seed to 1710653435
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.NormalDihedralWorks (44 ms)
56: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.003 0.002 188.5
56: (ns/day) (hour/ns)
56: Performance: 54.388 0.441
56: Setting the LD random seed to -722206867
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (63 ms)
56: [----------] 6 tests from BondedInteractionsTest (269 ms total)
56:
56: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest
56: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0
56: Number of degrees of freedom in T-Coupling group rest is 10.00
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'Dipoles'
56: 20 steps, 0.1 ps.
56: Setting the LD random seed to -845172817
56:
56: Generated 1 of the 1 non-bonded parameter combinations
56:
56: Excluding 1 bonded neighbours molecule type 'Dipole'
56:
56: Searching the wall atom type(s)
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200
56:
56: Estimate for the relative computational load of the PME mesh part: 1.00
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 1.075 0.538 199.8
56: (ns/day) (hour/ns)
56: Performance: 8.430 2.847
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision)
56:
56: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (40892 ms)
56: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1
56: Test system 'epsilon-surface-constraint' cannot run with 1 ranks.
56: The supported numbers are > 1.
56: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms)
56: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: With epsilon_surface > 0 all molecules should be neutral.
56:
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: With epsilon_surface > 0 you can only use domain decomposition when there
56: are only small molecules with all bonds constrained (mdrun will check for
56: this).
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 4 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'Dipoles'
56: 20 steps, 0.1 ps.
56: Setting the LD random seed to 2130689495
56:
56: Generated 1 of the 1 non-bonded parameter combinations
56:
56: Excluding 1 bonded neighbours molecule type 'Dipole'
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200
56:
56: Estimate for the relative computational load of the PME mesh part: 1.00
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.483 0.242 199.7
56: (ns/day) (hour/ns)
56: Performance: 18.769 1.279
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Last energy frame read 5 time 0.050
56: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (16786 ms)
56: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (57680 ms total)
56:
56: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest
56: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -181412993
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.964 0.482 199.8
56: (ns/day) (hour/ns)
56: Performance: 0.896 26.798
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -537019443
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.333 0.167 199.5
56: (ns/day) (hour/ns)
56: Performance: 2.589 9.268
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004
56:
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (24680 ms)
56: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -33887492
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.333 0.167 199.5
56: (ns/day) (hour/ns)
56: Performance: 2.586 9.282
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -1107430955
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.367 0.184 199.5
56: (ns/day) (hour/ns)
56: Performance: 2.351 10.208
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004
56:
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (618 ms)
56: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (25299 ms total)
56:
56: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest
56: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0
56: Generating 1-4 interactions: fudge = 0.5
56: Pull group 1 'FirstWaterMolecule' has 3 atoms
56: Pull group 2 'SecondWaterMolecule' has 3 atoms
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56: Pull group natoms pbc atom distance at start reference at t=0
56: 1 3 2
56: 2 3 5 1.112 nm 1.000 nm
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting mdrun 'spc2'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to 2075655165
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Generated 3 of the 3 1-4 parameter combinations
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning H bonds into constraints...
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.453 0.227 199.7
56: (ns/day) (hour/ns)
56: Performance: 1.904 12.602
56: Generating 1-4 interactions: fudge = 0.5
56: Pull group 1 'FirstWaterMolecule' has 3 atoms
56: Pull group 2 'SecondWaterMolecule' has 3 atoms
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56: Pull group natoms pbc atom distance at start reference at t=0
56: 1 3 2
56: 2 3 5 1.112 nm 1.000 nm
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting mdrun 'spc2'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -276899866
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Generated 3 of the 3 1-4 parameter combinations
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning H bonds into constraints...
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.485 0.243 199.7
56: (ns/day) (hour/ns)
56: Performance: 1.779 13.489
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004
56:
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (550 ms)
56: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (550 ms total)
56:
56: [----------] Global test environment tear-down
56: [==========] 14 tests from 6 test cases ran. (96979 ms total)
56: [ PASSED ] 14 tests.
56/65 Test #56: MdrunTests ............................ Passed 97.06 sec
test 57
Start 57: MdrunPmeTests
57: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-pme-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunPmeTests.xml"
57: Test timeout computed to be: 600
57: [==========] Running 3 tests from 1 test case.
57: [----------] Global test environment set-up.
57: [----------] 3 tests from PmeTest
57: [ RUN ] PmeTest.ReproducesEnergies
57: Number of degrees of freedom in T-Coupling group rest is 12.00
57:
57: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
57: NVE simulation: will use the initial temperature of 1046.791 K for
57: determining the Verlet buffer size
57:
57:
57: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
57: The optimal PME mesh load for parallel simulations is below 0.5
57: and for highly parallel simulations between 0.25 and 0.33,
57: for higher performance, increase the cut-off and the PME grid spacing.
57:
57:
57:
57: There were 2 notes
57: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 20 steps, 0.0 ps.
57: Setting the LD random seed to -564985891
57:
57: Generated 8 of the 10 non-bonded parameter combinations
57:
57: Excluding 2 bonded neighbours molecule type 'Methanol'
57:
57: Excluding 2 bonded neighbours molecule type 'SOL'
57:
57: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
57:
57: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
57:
57: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
57:
57: Note that mdrun will redetermine rlist based on the actual pair-list setup
57: Calculating fourier grid dimensions for X Y Z
57: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
57:
57: Estimate for the relative computational load of the PME mesh part: 1.00
57:
57: This run will generate roughly 0 Mb of data
57:
57: Writing final coordinates.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.589 0.295 199.8
57: (ns/day) (hour/ns)
57: Performance: 6.151 3.901
57: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
57:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 20 steps, 0.0 ps.
57:
57: Writing final coordinates.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.489 0.245 199.8
57: (ns/day) (hour/ns)
57: Performance: 7.414 3.237
57: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
57:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57:
57: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
57: starting mdrun 'spc-and-methanol'
57: 20 steps, 0.0 ps.
57:
57: Writing final coordinates.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.630 0.315 199.8
57: (ns/day) (hour/ns)
57: Performance: 5.752 4.173
57: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
57:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (11792 ms)
57: [ RUN ] PmeTest.ScalesTheBox
57:
57: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
57: For a correct single-point energy evaluation with nsteps = 0, use
57: continuation = yes to avoid constraining the input coordinates.
57:
57: Number of degrees of freedom in T-Coupling group rest is 12.00
57:
57: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
57: NVE simulation: will use the initial temperature of 1046.791 K for
57: determining the Verlet buffer size
57:
57:
57: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
57: The optimal PME mesh load for parallel simulations is below 0.5
57: and for highly parallel simulations between 0.25 and 0.33,
57: for higher performance, increase the cut-off and the PME grid spacing.
57:
57:
57:
57: There were 3 notes
57: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 0 steps, 0.0 ps.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.013 0.007 191.2
57: (ns/day) (hour/ns)
57: Performance: 12.426 1.931
57: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
57:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 1659338607
57:
57: Generated 8 of the 10 non-bonded parameter combinations
57:
57: Excluding 2 bonded neighbours molecule type 'Methanol'
57:
57: Excluding 2 bonded neighbours molecule type 'SOL'
57:
57: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
57:
57: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
57:
57: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
57:
57: Note that mdrun will redetermine rlist based on the actual pair-list setup
57: Calculating fourier grid dimensions for X Y Z
57: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
57:
57: Estimate for the relative computational load of the PME mesh part: 1.00
57:
57: This run will generate roughly 0 Mb of data
57: [ OK ] PmeTest.ScalesTheBox (101 ms)
57: [ RUN ] PmeTest.ScalesTheBoxWithWalls
57:
57: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
57: For a correct single-point energy evaluation with nsteps = 0, use
57: continuation = yes to avoid constraining the input coordinates.
57:
57: Number of degrees of freedom in T-Coupling group rest is 13.00
57:
57: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
57: NVE simulation: will use the initial temperature of 966.268 K for
57: determining the Verlet buffer size
57:
57:
57: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
57: The optimal PME mesh load for parallel simulations is below 0.5
57: and for highly parallel simulations between 0.25 and 0.33,
57: for higher performance, increase the cut-off and the PME grid spacing.
57:
57:
57:
57: There were 3 notes
57: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 0 steps, 0.0 ps.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.049 0.025 196.7
57: (ns/day) (hour/ns)
57: Performance: 3.434 6.990
57: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
57:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -247726338
57:
57: Generated 8 of the 10 non-bonded parameter combinations
57:
57: Excluding 2 bonded neighbours molecule type 'Methanol'
57:
57: Excluding 2 bonded neighbours molecule type 'SOL'
57:
57: Searching the wall atom type(s)
57:
57: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
57:
57: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
57:
57: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
57:
57: Note that mdrun will redetermine rlist based on the actual pair-list setup
57: Calculating fourier grid dimensions for X Y Z
57: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
57:
57: Estimate for the relative computational load of the PME mesh part: 1.00
57:
57: This run will generate roughly 0 Mb of data
57: [ OK ] PmeTest.ScalesTheBoxWithWalls (33090 ms)
57: [----------] 3 tests from PmeTest (44983 ms total)
57:
57: [----------] Global test environment tear-down
57: [==========] 3 tests from 1 test case ran. (45022 ms total)
57: [ PASSED ] 3 tests.
57/65 Test #57: MdrunPmeTests ......................... Passed 45.09 sec
test 58
Start 58: MdrunNonIntegratorTests
58: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml"
58: Test timeout computed to be: 600
58: [==========] Running 58 tests from 5 test cases.
58: [----------] Global test environment set-up.
58: [----------] 1 test from NonbondedBenchTest
58: [ RUN ] NonbondedBenchTest.BasicEndToEndTest
58: System size: 3000 atoms
58: Cut-off radius: 1 nm
58: Number of threads: 1
58: Number of iterations: 1
58: Compute energies: no
58: Ewald excl. corr.: analytical
58:
58: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle
58: total useful
58: Ewald all geom. no 0.000 0.0000 inf inf
58: [ OK ] NonbondedBenchTest.BasicEndToEndTest (667 ms)
58: [----------] 1 test from NonbondedBenchTest (667 ms total)
58:
58: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -4.7990997e+01
58: Maximum force = 1.8629761e+02 on atom 13
58: Norm of force = 8.7722009e+01
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (3433 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 3.02331e+02 on atom 3
58: F-Norm = 1.18024e+02
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -5.5862339e+01
58: Maximum force = 4.2727011e+02 on atom 13
58: Norm of force = 1.8452841e+02
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (3216 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 22.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 3.1937714e+02
58: Maximum force = 9.9988643e+03 on atom 9
58: Norm of force = 4.6166996e+03
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: turning H bonds into constraints...
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (984 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58:
58: NOTE 3 [file glycine_vacuo.top, line 12]:
58: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
58:
58: Number of degrees of freedom in T-Coupling group System is 22.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 2.41575e+04 on atom 10
58: F-Norm = 1.18451e+04
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 1.5174377e+02
58: Maximum force = 7.4208838e+03 on atom 9
58: Norm of force = 3.5693005e+03
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: turning H bonds into constraints...
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (977 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -1.5698413e+02
58: Maximum force = 4.5704984e+02 on atom 17
58: Norm of force = 1.8327747e+02
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (110 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58:
58: NOTE 4 [file unknown]:
58: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 5 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 1.06801e+03 on atom 28
58: F-Norm = 4.26916e+02
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -1.6941180e+02
58: Maximum force = 2.1832491e+02 on atom 17
58: Norm of force = 7.9220732e+01
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (112 ms)
58: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (8832 ms total)
58:
58: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents converged to Fmax < 10 in 1 steps
58: Potential Energy = -9.7425699e-01
58: Maximum force = 4.0132303e+00 on atom 1
58: Norm of force = 1.6383944e+00
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (36 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 4.01323e+00 on atom 1
58: F-Norm = 1.63839e+00
58:
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
58: Potential Energy = -9.9064207e-01
58: Maximum force = 2.5781622e+00 on atom 1
58: Norm of force = 1.0525302e+00
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (36 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58:
58: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58:
58: There was 1 warning
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Low-Memory BFGS Minimizer:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: Using 10 BFGS correction steps.
58:
58: F-max = 4.01323e+00 on atom 1
58: F-Norm = 1.63839e+00
58:
58:
58: writing lowest energy coordinates.
58:
58: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
58: Potential Energy = -9.9064207e-01
58: Maximum force = 2.5781622e+00 on atom 1
58: Norm of force = 1.0525302e+00
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (37 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 3.1939697e+02
58: Maximum force = 9.9704248e+03 on atom 9
58: Norm of force = 4.6227540e+03
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (981 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 2.41672e+04 on atom 10
58: F-Norm = 1.19357e+04
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 1.5625757e+02
58: Maximum force = 7.5018242e+03 on atom 9
58: Norm of force = 3.6139019e+03
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (984 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58:
58: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58:
58: There was 1 warning
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Low-Memory BFGS Minimizer:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: Using 10 BFGS correction steps.
58:
58: F-max = 2.41672e+04 on atom 10
58: F-Norm = 1.19357e+04
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 5.6111725e+02
58: Maximum force = 1.2685491e+04 on atom 10
58: Norm of force = 6.0643622e+03
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (985 ms)
58: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (3059 ms total)
58:
58: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
58: NVE simulation: will use the initial temperature of 68.810 K for
58: determining the Verlet buffer size
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.947 0.474 199.9
58: (ns/day) (hour/ns)
58: Performance: 3.100 7.741
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr'
58:
58: trr version: GMX_trn_file (single precision)
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.006 0.003 193.1
58: (ns/day) (hour/ns)
58: Performance: 492.769 0.049
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (528 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
58: NVE simulation: will use the initial temperature of 68.810 K for
58: determining the Verlet buffer size
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.403 0.202 199.9
58: (ns/day) (hour/ns)
58: Performance: 7.282 3.296
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.006 0.003 192.7
58: (ns/day) (hour/ns)
58: Performance: 497.826 0.048
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (257 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.444 0.222 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.603 3.635
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.007 0.004 193.6
58: (ns/day) (hour/ns)
58: Performance: 409.859 0.059
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (279 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.482 0.241 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.085 3.944
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.007 0.003 193.4
58: (ns/day) (hour/ns)
58: Performance: 423.875 0.057
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (302 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: NVE simulation: will use the initial temperature of 398.997 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.478 0.239 199.7
58: (ns/day) (hour/ns)
58: Performance: 6.137 3.911
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.007 0.004 193.8
58: (ns/day) (hour/ns)
58: Performance: 392.920 0.061
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (3506 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: NVE simulation: will use the initial temperature of 398.997 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.493 0.247 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.950 4.034
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.007 0.004 193.9
58: (ns/day) (hour/ns)
58: Performance: 391.895 0.061
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (3484 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.400 0.200 199.7
58: (ns/day) (hour/ns)
58: Performance: 7.326 3.276
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.007 0.004 193.9
58: (ns/day) (hour/ns)
58: Performance: 392.469 0.061
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (3470 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.422 0.211 199.7
58: (ns/day) (hour/ns)
58: Performance: 6.946 3.455
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.007 0.003 193.1
58: (ns/day) (hour/ns)
58: Performance: 427.581 0.056
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (3761 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: NVE simulation: will use the initial temperature of 456.887 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 6 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.393 0.197 199.6
58: (ns/day) (hour/ns)
58: Performance: 7.454 3.220
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.010 0.005 194.6
58: (ns/day) (hour/ns)
58: Performance: 282.221 0.085
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (348 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: NVE simulation: will use the initial temperature of 456.887 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 6 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.449 0.225 199.6
58: (ns/day) (hour/ns)
58: Performance: 6.537 3.672
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.010 0.005 194.5
58: (ns/day) (hour/ns)
58: Performance: 283.467 0.085
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (375 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 5 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 1.065 0.533 199.9
58: (ns/day) (hour/ns)
58: Performance: 2.757 8.706
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.011 0.006 194.8
58: (ns/day) (hour/ns)
58: Performance: 257.981 0.093
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (847 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 5 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.490 0.245 199.7
58: (ns/day) (hour/ns)
58: Performance: 5.990 4.007
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.006 195.8
58: (ns/day) (hour/ns)
58: Performance: 228.763 0.105
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (492 ms)
58: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (17650 ms total)
58:
58: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.529 0.265 199.6
58: (ns/day) (hour/ns)
58: Performance: 5.543 4.330
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 188.2
58: (ns/day) (hour/ns)
58: Performance: 220.620 0.109
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (410 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.490 0.246 199.6
58: (ns/day) (hour/ns)
58: Performance: 5.979 4.014
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.012 0.007 185.7
58: (ns/day) (hour/ns)
58: Performance: 220.116 0.109
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (389 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.535 0.268 199.7
58: (ns/day) (hour/ns)
58: Performance: 5.481 4.379
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.014 0.008 188.6
58: (ns/day) (hour/ns)
58: Performance: 192.308 0.125
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (412 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.576 0.288 199.7
58: (ns/day) (hour/ns)
58: Performance: 5.093 4.712
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 187.8
58: (ns/day) (hour/ns)
58: Performance: 204.596 0.117
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (436 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.544 0.272 199.7
58: (ns/day) (hour/ns)
58: Performance: 5.391 4.451
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 186.5
58: (ns/day) (hour/ns)
58: Performance: 205.175 0.117
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (424 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.497 0.249 199.6
58: (ns/day) (hour/ns)
58: Performance: 5.898 4.069
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 186.1
58: (ns/day) (hour/ns)
58: Performance: 203.589 0.118
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (400 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.493 0.247 199.6
58: (ns/day) (hour/ns)
58: Performance: 5.944 4.037
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 187.6
58: (ns/day) (hour/ns)
58: Performance: 204.718 0.117
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (400 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.495 0.248 199.6
58: (ns/day) (hour/ns)
58: Performance: 5.925 4.050
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 186.6
58: (ns/day) (hour/ns)
58: Performance: 204.657 0.117
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (399 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.473 0.237 199.6
58: (ns/day) (hour/ns)
58: Performance: 6.194 3.875
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 187.7
58: (ns/day) (hour/ns)
58: Performance: 206.316 0.116
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (389 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.495 0.248 199.6
58: (ns/day) (hour/ns)
58: Performance: 5.918 4.056
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 187.7
58: (ns/day) (hour/ns)
58: Performance: 206.219 0.116
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (398 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.502 0.251 199.6
58: (ns/day) (hour/ns)
58: Performance: 5.843 4.107
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.019 0.010 191.2
58: (ns/day) (hour/ns)
58: Performance: 148.667 0.161
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (399 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.601 0.301 199.9
58: (ns/day) (hour/ns)
58: Performance: 4.884 4.914
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.016 0.008 189.5
58: (ns/day) (hour/ns)
58: Performance: 175.876 0.136
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (447 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.604 0.302 199.9
58: (ns/day) (hour/ns)
58: Performance: 4.863 4.936
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.014 0.008 189.2
58: (ns/day) (hour/ns)
58: Performance: 192.717 0.125
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (469 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.690 0.345 199.9
58: (ns/day) (hour/ns)
58: Performance: 4.254 5.641
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 186.8
58: (ns/day) (hour/ns)
58: Performance: 216.732 0.111
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (528 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.529 0.265 199.8
58: (ns/day) (hour/ns)
58: Performance: 5.546 4.327
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 187.0
58: (ns/day) (hour/ns)
58: Performance: 216.336 0.111
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (409 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.510 0.255 199.8
58: (ns/day) (hour/ns)
58: Performance: 5.752 4.172
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 190.0
58: (ns/day) (hour/ns)
58: Performance: 165.478 0.145
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (402 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.595 0.298 199.8
58: (ns/day) (hour/ns)
58: Performance: 4.935 4.864
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 187.2
58: (ns/day) (hour/ns)
58: Performance: 213.073 0.113
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (442 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.533 0.267 199.8
58: (ns/day) (hour/ns)
58: Performance: 5.505 4.360
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 186.8
58: (ns/day) (hour/ns)
58: Performance: 216.078 0.111
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (411 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.555 0.278 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.290 4.536
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 187.1
58: (ns/day) (hour/ns)
58: Performance: 217.843 0.110
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (422 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.565 0.283 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.196 4.619
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.015 0.008 188.6
58: (ns/day) (hour/ns)
58: Performance: 187.503 0.128
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (444 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.606 0.303 199.9
58: (ns/day) (hour/ns)
58: Performance: 4.843 4.956
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.014 0.007 188.0
58: (ns/day) (hour/ns)
58: Performance: 202.033 0.119
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (452 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.524 0.262 199.8
58: (ns/day) (hour/ns)
58: Performance: 5.598 4.288
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.014 0.007 187.9
58: (ns/day) (hour/ns)
58: Performance: 201.630 0.119
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (411 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.534 0.268 199.5
58: (ns/day) (hour/ns)
58: Performance: 5.486 4.375
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 187.2
58: (ns/day) (hour/ns)
58: Performance: 214.110 0.112
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (503 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.647 0.324 199.7
58: (ns/day) (hour/ns)
58: Performance: 4.532 5.296
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 187.1
58: (ns/day) (hour/ns)
58: Performance: 213.310 0.113
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (553 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.540 0.271 199.7
58: (ns/day) (hour/ns)
58: Performance: 5.427 4.422
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.021 0.011 191.5
58: (ns/day) (hour/ns)
58: Performance: 136.568 0.176
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (504 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.957 0.479 199.8
58: (ns/day) (hour/ns)
58: Performance: 3.068 7.824
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 183.1
58: (ns/day) (hour/ns)
58: Performance: 202.678 0.118
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (711 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.495 0.248 199.7
58: (ns/day) (hour/ns)
58: Performance: 5.922 4.052
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 186.8
58: (ns/day) (hour/ns)
58: Performance: 219.402 0.109
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (481 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.544 0.272 199.7
58: (ns/day) (hour/ns)
58: Performance: 5.393 4.451
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 187.0
58: (ns/day) (hour/ns)
58: Performance: 212.464 0.113
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (518 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.500 0.250 199.7
58: (ns/day) (hour/ns)
58: Performance: 5.865 4.092
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.014 0.008 188.4
58: (ns/day) (hour/ns)
58: Performance: 191.937 0.125
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (505 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.475 0.238 199.6
58: (ns/day) (hour/ns)
58: Performance: 6.167 3.892
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.014 0.007 188.0
58: (ns/day) (hour/ns)
58: Performance: 197.487 0.122
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (477 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 1.252 0.627 199.9
58: (ns/day) (hour/ns)
58: Performance: 2.344 10.237
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.014 0.007 188.1
58: (ns/day) (hour/ns)
58: Performance: 197.880 0.121
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (940 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.488 0.244 199.6
58: (ns/day) (hour/ns)
58: Performance: 6.015 3.990
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.014 0.008 188.2
58: (ns/day) (hour/ns)
58: Performance: 195.786 0.123
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (493 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.502 0.251 199.7
58: (ns/day) (hour/ns)
58: Performance: 5.847 4.105
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.014 0.008 189.0
58: (ns/day) (hour/ns)
58: Performance: 193.274 0.124
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (496 ms)
58: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (15478 ms total)
58:
58: [----------] Global test environment tear-down
58: [==========] 58 tests from 5 test cases ran. (45832 ms total)
58: [ PASSED ] 58 tests.
58/65 Test #58: MdrunNonIntegratorTests ............... Passed 45.92 sec
test 59
Start 59: MdrunTpiTests
59: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunTpiTests.xml"
59: Test timeout computed to be: 600
59: [==========] Running 2 tests from 1 test case.
59: [----------] Global test environment set-up.
59: [----------] 2 tests from Simple/TpiTest
59: [ RUN ] Simple/TpiTest.ReproducesOutput/0
59: Ignoring obsolete mdp entry 'ns_type'
59: Generating 1-4 interactions: fudge = 0.5
59: Number of degrees of freedom in T-Coupling group System is 1308.00
59: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
59: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
59: TPI is not implemented for GPUs.
59:
59: Using 1 MPI thread
59: Using 1 OpenMP thread
59:
59:
59: NOTE: Thread affinity was not set.
59:
59: WARNING: Using the slow plain C kernels. This should
59: not happen during routine usage on supported platforms.
59: Reading frames from gro file '216 water molecules', 648 atoms.
59:
Reading frame 0 time 0.000 mu 8.706e+02 <mu> 8.706e+02
59:
Last frame 0 time 0.000
59: Generated 331705 of the 331705 non-bonded parameter combinations
59:
59: Generated 331705 of the 331705 1-4 parameter combinations
59:
59: Excluding 2 bonded neighbours molecule type 'SOL'
59:
59: Excluding 3 bonded neighbours molecule type 'methane'
59: Analysing residue names:
59: There are: 216 Water residues
59: There are: 1 Other residues
59: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
59:
59: This run will generate roughly 0 Mb of data
59: [ OK ] Simple/TpiTest.ReproducesOutput/0 (3608 ms)
59: [ RUN ] Simple/TpiTest.ReproducesOutput/1
59: Ignoring obsolete mdp entry 'ns_type'
59: Generating 1-4 interactions: fudge = 0.5
59: Number of degrees of freedom in T-Coupling group System is 1308.00
59: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
59: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
59: TPI is not implemented for GPUs.
59:
59: Using 1 MPI thread
59: Using 1 OpenMP thread
59:
59:
59: NOTE: Thread affinity was not set.
59:
59: WARNING: Using the slow plain C kernels. This should
59: not happen during routine usage on supported platforms.
59: Reading frames from gro file '216 water molecules', 648 atoms.
59:
Reading frame 0 time 0.000 mu 9.144e+01 <mu> 9.144e+01
59:
Last frame 0 time 0.000
59: Generated 331705 of the 331705 non-bonded parameter combinations
59:
59: Generated 331705 of the 331705 1-4 parameter combinations
59:
59: Excluding 2 bonded neighbours molecule type 'SOL'
59:
59: Excluding 3 bonded neighbours molecule type 'methane'
59: Analysing residue names:
59: There are: 216 Water residues
59: There are: 1 Other residues
59: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
59:
59: This run will generate roughly 0 Mb of data
59: [ OK ] Simple/TpiTest.ReproducesOutput/1 (3596 ms)
59: [----------] 2 tests from Simple/TpiTest (7204 ms total)
59:
59: [----------] Global test environment tear-down
59: [==========] 2 tests from 1 test case ran. (7242 ms total)
59: [ PASSED ] 2 tests.
59/65 Test #59: MdrunTpiTests ......................... Passed 7.32 sec
test 60
Start 60: MdrunMpiTests
60: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiTests.xml"
60: Test timeout computed to be: 600
60: [==========] Running 22 tests from 7 test cases.
60: [----------] Global test environment set-up.
60: [----------] 1 test from DomainDecompositionSpecialCasesTest
60: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 9.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc2'
60: 0 steps, 0.0 ps.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.004 0.001 279.7
60: (ns/day) (hour/ns)
60: Performance: 63.321 0.379
60: Setting the LD random seed to -1216741550
60:
60: Generated 3 of the 3 non-bonded parameter combinations
60:
60: Generated 3 of the 3 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (46 ms)
60: [----------] 1 test from DomainDecompositionSpecialCasesTest (46 ms total)
60:
60: [----------] 4 tests from MimicTest
60: [ RUN ] MimicTest.OneQuantumMol
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 21.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
60:
60: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 2.589 0.677 382.3
60: (ns/day) (hour/ns)
60: Performance: 0.128 188.135
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -4981805
60:
60: Generated 10 of the 10 non-bonded parameter combinations
60:
60: Generated 10 of the 10 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.OneQuantumMol (2078 ms)
60: [ RUN ] MimicTest.AllQuantumMol
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 21.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
60:
60: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 2.590 0.677 382.3
60: (ns/day) (hour/ns)
60: Performance: 0.128 188.161
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -715653289
60:
60: Generated 10 of the 10 non-bonded parameter combinations
60:
60: Generated 10 of the 10 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.AllQuantumMol (2073 ms)
60: [ RUN ] MimicTest.TwoQuantumMol
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 21.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
60:
60: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 2.530 0.662 381.9
60: (ns/day) (hour/ns)
60: Performance: 0.130 183.996
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -117705065
60:
60: Generated 10 of the 10 non-bonded parameter combinations
60:
60: Generated 10 of the 10 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.TwoQuantumMol (2044 ms)
60: [ RUN ] MimicTest.BondCuts
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 66.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
60: NVE simulation: will use the initial temperature of 300.368 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
60:
60: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 2.489 0.652 381.6
60: (ns/day) (hour/ns)
60: Performance: 0.132 181.213
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -270942988
60:
60: Generated 2211 of the 2211 non-bonded parameter combinations
60:
60: Generated 2211 of the 2211 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.BondCuts (2088 ms)
60: [----------] 4 tests from MimicTest (8287 ms total)
60:
60: [----------] 1 test from MultiSimTerminationTest
60: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
60: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (1 ms)
60: [----------] 1 test from MultiSimTerminationTest (1 ms total)
60:
60: [----------] 1 test from ReplicaExchangeTerminationTest
60: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
60: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
60: [----------] 1 test from ReplicaExchangeTerminationTest (1 ms total)
60:
60: [----------] 3 tests from PmeTest
60: [ RUN ] PmeTest.ReproducesEnergies
60: Number of degrees of freedom in T-Coupling group rest is 12.00
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
60: NVE simulation: will use the initial temperature of 1046.791 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
60: The optimal PME mesh load for parallel simulations is below 0.5
60: and for highly parallel simulations between 0.25 and 0.33,
60: for higher performance, increase the cut-off and the PME grid spacing.
60:
60:
60:
60: There were 2 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 20 steps, 0.0 ps.
60: Setting the LD random seed to -538460162
60:
60: Generated 8 of the 10 non-bonded parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'Methanol'
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60: Calculating fourier grid dimensions for X Y Z
60: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
60:
60: Estimate for the relative computational load of the PME mesh part: 1.00
60:
60: This run will generate roughly 0 Mb of data
60:
60: Writing final coordinates.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 8.281 2.110 392.5
60: (ns/day) (hour/ns)
60: Performance: 0.860 27.906
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 20 steps, 0.0 ps.
60:
60: Writing final coordinates.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 8.385 2.135 392.8
60: (ns/day) (hour/ns)
60: Performance: 0.850 28.238
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
60: starting mdrun 'spc-and-methanol'
60: 20 steps, 0.0 ps.
60:
60: Writing final coordinates.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 8.027 2.045 392.6
60: (ns/day) (hour/ns)
60: Performance: 0.887 27.047
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (29753 ms)
60: [ RUN ] PmeTest.ScalesTheBox
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Number of degrees of freedom in T-Coupling group rest is 12.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
60: NVE simulation: will use the initial temperature of 1046.791 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
60: The optimal PME mesh load for parallel simulations is below 0.5
60: and for highly parallel simulations between 0.25 and 0.33,
60: for higher performance, increase the cut-off and the PME grid spacing.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 0 steps, 0.0 ps.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.401 0.140 286.5
60: (ns/day) (hour/ns)
60: Performance: 0.618 38.838
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 2063547391
60:
60: Generated 8 of the 10 non-bonded parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'Methanol'
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60: Calculating fourier grid dimensions for X Y Z
60: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
60:
60: Estimate for the relative computational load of the PME mesh part: 1.00
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] PmeTest.ScalesTheBox (1119 ms)
60: [ RUN ] PmeTest.ScalesTheBoxWithWalls
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Number of degrees of freedom in T-Coupling group rest is 13.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
60: NVE simulation: will use the initial temperature of 966.268 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
60: The optimal PME mesh load for parallel simulations is below 0.5
60: and for highly parallel simulations between 0.25 and 0.33,
60: for higher performance, increase the cut-off and the PME grid spacing.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 0 steps, 0.0 ps.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.611 0.192 317.6
60: (ns/day) (hour/ns)
60: Performance: 0.449 53.418
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -1141041189
60:
60: Generated 8 of the 10 non-bonded parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'Methanol'
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: Searching the wall atom type(s)
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60: Calculating fourier grid dimensions for X Y Z
60: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
60:
60: Estimate for the relative computational load of the PME mesh part: 1.00
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] PmeTest.ScalesTheBoxWithWalls (63410 ms)
60: [----------] 3 tests from PmeTest (94282 ms total)
60:
60: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -4.7990929e+01
60: Maximum force = 1.8629704e+02 on atom 13
60: Norm of force = 8.7721907e+01
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
60:
60: Generated 330891 of the 330891 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (6313 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 3.02331e+02 on atom 3
60: F-Norm = 1.18024e+02
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -5.5862312e+01
60: Maximum force = 4.2726910e+02 on atom 13
60: Norm of force = 1.8452761e+02
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
60:
60: Generated 330891 of the 330891 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (7810 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 22.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 3.1937704e+02
60: Maximum force = 9.9988633e+03 on atom 9
60: Norm of force = 4.6166993e+03
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: turning H bonds into constraints...
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (4129 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60:
60: NOTE 3 [file glycine_vacuo.top, line 12]:
60: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
60:
60: Number of degrees of freedom in T-Coupling group System is 22.00
60:
60: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 4 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 2.41575e+04 on atom 10
60: F-Norm = 1.18451e+04
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 1.5174442e+02
60: Maximum force = 7.4208892e+03 on atom 9
60: Norm of force = 3.5693002e+03
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: turning H bonds into constraints...
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (5690 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60:
60: NOTE 3 [file unknown]:
60: You are using constraints on all bonds, whereas the forcefield has been
60: parametrized only with constraints involving hydrogen atoms. We suggest
60: using constraints = h-bonds instead, this will also improve performance.
60:
60: Number of degrees of freedom in T-Coupling group System is 23.00
60:
60: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 4 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -1.5698419e+02
60: Maximum force = 4.5704996e+02 on atom 17
60: Norm of force = 1.8327748e+02
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations
60:
60: Generated 2145 of the 2145 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
60:
60: turning all bonds into constraints...
60:
60: Cleaning up constraints and constant bonded interactions with virtual sites
60:
60: Removed 18 Angles with virtual sites, 21 left
60:
60: Removed 10 Proper Dih.s with virtual sites, 44 left
60:
60: Converted 15 Constraints with virtual sites to connections, 7 left
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (4790 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60:
60: NOTE 3 [file unknown]:
60: You are using constraints on all bonds, whereas the forcefield has been
60: parametrized only with constraints involving hydrogen atoms. We suggest
60: using constraints = h-bonds instead, this will also improve performance.
60:
60:
60: NOTE 4 [file unknown]:
60: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
60:
60: Number of degrees of freedom in T-Coupling group System is 23.00
60:
60: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 5 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 1.06801e+03 on atom 28
60: F-Norm = 4.26916e+02
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -1.6941193e+02
60: Maximum force = 2.1835349e+02 on atom 17
60: Norm of force = 7.9216550e+01
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations
60:
60: Generated 2145 of the 2145 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
60:
60: turning all bonds into constraints...
60:
60: Cleaning up constraints and constant bonded interactions with virtual sites
60:
60: Removed 18 Angles with virtual sites, 21 left
60:
60: Removed 10 Proper Dih.s with virtual sites, 44 left
60:
60: Converted 15 Constraints with virtual sites to connections, 7 left
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (7052 ms)
60: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (35784 ms total)
60:
60: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Number of degrees of freedom in T-Coupling group System is 33.00
60:
60: There were 2 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents converged to Fmax < 10 in 1 steps
60: Potential Energy = -9.7425699e-01
60: Maximum force = 4.0132303e+00 on atom 3
60: Norm of force = 1.6383944e+00
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
60:
60: Excluding 1 bonded neighbours molecule type 'Argon'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (1602 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Number of degrees of freedom in T-Coupling group System is 33.00
60:
60: There were 2 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 4.01323e+00 on atom 3
60: F-Norm = 1.63839e+00
60:
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
60: Potential Energy = -9.9064207e-01
60: Maximum force = 2.5781622e+00 on atom 3
60: Norm of force = 1.0525302e+00
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
60:
60: Excluding 1 bonded neighbours molecule type 'Argon'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (2139 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60:
60: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
60:
60: Number of degrees of freedom in T-Coupling group System is 33.00
60:
60: There were 2 notes
60:
60: There was 1 warning
60: Generated 1 of the 1 non-bonded parameter combinations
60:
60: Excluding 1 bonded neighbours molecule type 'Argon'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (22 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 3.1939685e+02
60: Maximum force = 9.9704248e+03 on atom 9
60: Norm of force = 4.6227568e+03
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (3810 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 2.41672e+04 on atom 10
60: F-Norm = 1.19357e+04
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 1.5625764e+02
60: Maximum force = 7.5018237e+03 on atom 9
60: Norm of force = 3.6139019e+03
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (5330 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60:
60: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60:
60: There was 1 warning
60: Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (947 ms)
60: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (13851 ms total)
60:
60: [----------] Global test environment tear-down
60: [==========] 22 tests from 7 test cases ran. (152521 ms total)
60: [ PASSED ] 22 tests.
60:
60: YOU HAVE 4 DISABLED TESTS
60:
60/65 Test #60: MdrunMpiTests ......................... Passed 152.60 sec
test 61
Start 61: MdrunMpiPmeTests
61: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiPmeTests.xml"
61: Test timeout computed to be: 600
61: [==========] Running 3 tests from 1 test case.
61: [----------] Global test environment set-up.
61: [----------] 3 tests from PmeTest
61: [ RUN ] PmeTest.ReproducesEnergies
61: Number of degrees of freedom in T-Coupling group rest is 12.00
61:
61: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
61: NVE simulation: will use the initial temperature of 1046.791 K for
61: determining the Verlet buffer size
61:
61:
61: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
61: The optimal PME mesh load for parallel simulations is below 0.5
61: and for highly parallel simulations between 0.25 and 0.33,
61: for higher performance, increase the cut-off and the PME grid spacing.
61:
61:
61:
61: There were 2 notes
61: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 20 steps, 0.0 ps.
61: Setting the LD random seed to -240408834
61:
61: Generated 8 of the 10 non-bonded parameter combinations
61:
61: Excluding 2 bonded neighbours molecule type 'Methanol'
61:
61: Excluding 2 bonded neighbours molecule type 'SOL'
61:
61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
61:
61: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
61:
61: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
61:
61: Note that mdrun will redetermine rlist based on the actual pair-list setup
61: Calculating fourier grid dimensions for X Y Z
61: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
61:
61: Estimate for the relative computational load of the PME mesh part: 1.00
61:
61: This run will generate roughly 0 Mb of data
61:
61: Writing final coordinates.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 1.186 0.297 399.6
61: (ns/day) (hour/ns)
61: Performance: 6.113 3.926
61: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
61:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61:
61: Non-default thread affinity set, disabling internal thread affinity
61:
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 20 steps, 0.0 ps.
61:
61: Writing final coordinates.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 8.320 2.129 390.8
61: (ns/day) (hour/ns)
61: Performance: 0.852 28.164
61: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
61:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61:
61: Non-default thread affinity set, disabling internal thread affinity
61:
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61:
61: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
61: starting mdrun 'spc-and-methanol'
61: 20 steps, 0.0 ps.
61:
61: Writing final coordinates.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 8.217 2.097 391.8
61: (ns/day) (hour/ns)
61: Performance: 0.865 27.741
61: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
61:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (16581 ms)
61: [ RUN ] PmeTest.ScalesTheBox
61:
61: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
61: For a correct single-point energy evaluation with nsteps = 0, use
61: continuation = yes to avoid constraining the input coordinates.
61:
61: Number of degrees of freedom in T-Coupling group rest is 12.00
61:
61: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
61: NVE simulation: will use the initial temperature of 1046.791 K for
61: determining the Verlet buffer size
61:
61:
61: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
61: The optimal PME mesh load for parallel simulations is below 0.5
61: and for highly parallel simulations between 0.25 and 0.33,
61: for higher performance, increase the cut-off and the PME grid spacing.
61:
61:
61:
61: There were 3 notes
61: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61:
61: Non-default thread affinity set, disabling internal thread affinity
61:
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 0 steps, 0.0 ps.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.410 0.142 288.4
61: (ns/day) (hour/ns)
61: Performance: 0.608 39.502
61: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
61:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -2884365
61:
61: Generated 8 of the 10 non-bonded parameter combinations
61:
61: Excluding 2 bonded neighbours molecule type 'Methanol'
61:
61: Excluding 2 bonded neighbours molecule type 'SOL'
61:
61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
61:
61: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
61:
61: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
61:
61: Note that mdrun will redetermine rlist based on the actual pair-list setup
61: Calculating fourier grid dimensions for X Y Z
61: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
61:
61: Estimate for the relative computational load of the PME mesh part: 1.00
61:
61: This run will generate roughly 0 Mb of data
61: [ OK ] PmeTest.ScalesTheBox (1184 ms)
61: [ RUN ] PmeTest.ScalesTheBoxWithWalls
61:
61: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
61: For a correct single-point energy evaluation with nsteps = 0, use
61: continuation = yes to avoid constraining the input coordinates.
61:
61: Number of degrees of freedom in T-Coupling group rest is 13.00
61:
61: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
61: NVE simulation: will use the initial temperature of 966.268 K for
61: determining the Verlet buffer size
61:
61:
61: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
61: The optimal PME mesh load for parallel simulations is below 0.5
61: and for highly parallel simulations between 0.25 and 0.33,
61: for higher performance, increase the cut-off and the PME grid spacing.
61:
61:
61:
61: There were 3 notes
61: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61:
61: Non-default thread affinity set, disabling internal thread affinity
61:
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 0 steps, 0.0 ps.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.588 0.187 315.1
61: (ns/day) (hour/ns)
61: Performance: 0.463 51.853
61: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
61:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 2111168509
61:
61: Generated 8 of the 10 non-bonded parameter combinations
61:
61: Excluding 2 bonded neighbours molecule type 'Methanol'
61:
61: Excluding 2 bonded neighbours molecule type 'SOL'
61:
61: Searching the wall atom type(s)
61:
61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
61:
61: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
61:
61: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
61:
61: Note that mdrun will redetermine rlist based on the actual pair-list setup
61: Calculating fourier grid dimensions for X Y Z
61: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
61:
61: Estimate for the relative computational load of the PME mesh part: 1.00
61:
61: This run will generate roughly 0 Mb of data
61: [ OK ] PmeTest.ScalesTheBoxWithWalls (63546 ms)
61: [----------] 3 tests from PmeTest (81326 ms total)
61:
61: [----------] Global test environment tear-down
61: [==========] 3 tests from 1 test case ran. (81369 ms total)
61: [ PASSED ] 3 tests.
61/65 Test #61: MdrunMpiPmeTests ...................... Passed 81.44 sec
test 62
Start 62: MdrunMpiCoordinationTestsOneRank
62: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml"
62: Test timeout computed to be: 1920
62: [==========] Running 39 tests from 3 test cases.
62: [----------] Global test environment set-up.
62: [----------] 1 test from BasicPropagators/PeriodicActionsTest
62: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.224 0.224 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.557 3.660
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.214 0.215 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.831 3.513
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.224 0.224 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.546 3.666
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.190 0.191 99.6
62: (ns/day) (hour/ns)
62: Performance: 7.697 3.118
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.203 0.204 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.216 3.326
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.217 0.220 98.7
62: (ns/day) (hour/ns)
62: Performance: 6.674 3.596
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1537 ms)
62: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1538 ms total)
62:
62: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.189 0.189 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.764 3.091
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.243 0.243 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.040 3.974
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.240 0.240 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.111 3.927
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.229 0.229 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.410 3.744
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.241 0.242 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.074 3.951
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.217 0.217 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.761 3.550
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1634 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.192 0.193 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.628 3.147
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.199 0.200 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.351 3.265
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.195 0.195 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.524 3.190
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.199 0.199 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.365 3.259
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.209 0.212 98.8
62: (ns/day) (hour/ns)
62: Performance: 6.935 3.461
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.213 0.213 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.883 3.487
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1467 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.203 0.203 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.240 3.315
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.210 0.211 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.968 3.444
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.228 0.228 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.430 3.733
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.239 0.240 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.131 3.914
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.218 0.219 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.708 3.578
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.196 0.197 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.465 3.215
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1521 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.203 0.203 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.231 3.319
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.210 0.211 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.970 3.443
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.206 0.206 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.117 3.372
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.203 0.203 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.225 3.322
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.207 0.208 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.069 3.395
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.207 0.208 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.076 3.392
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1489 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.192 0.192 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.653 3.136
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.199 0.200 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.358 3.262
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.205 0.208 98.7
62: (ns/day) (hour/ns)
62: Performance: 7.070 3.395
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.200 0.200 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.329 3.275
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.199 0.200 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.348 3.266
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.299 0.300 99.8
62: (ns/day) (hour/ns)
62: Performance: 4.901 4.897
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1532 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.184 0.185 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.956 3.017
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.292 0.293 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.016 4.785
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.269 0.270 99.7
62: (ns/day) (hour/ns)
62: Performance: 5.434 4.417
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.194 0.195 99.6
62: (ns/day) (hour/ns)
62: Performance: 7.528 3.188
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.210 0.210 99.6
62: (ns/day) (hour/ns)
62: Performance: 6.982 3.437
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.718 0.719 99.9
62: (ns/day) (hour/ns)
62: Performance: 2.044 11.741
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (2090 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.238 0.238 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.164 3.894
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.244 0.245 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.002 3.999
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.242 0.243 99.5
62: (ns/day) (hour/ns)
62: Performance: 6.047 3.969
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.302 0.305 99.2
62: (ns/day) (hour/ns)
62: Performance: 4.815 4.984
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.199 0.200 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.345 3.267
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.621 0.622 99.9
62: (ns/day) (hour/ns)
62: Performance: 2.362 10.159
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (2077 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.184 0.184 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.983 3.006
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.192 0.193 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.621 3.149
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.192 0.193 99.6
62: (ns/day) (hour/ns)
62: Performance: 7.626 3.147
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.189 0.190 99.6
62: (ns/day) (hour/ns)
62: Performance: 7.727 3.106
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.192 0.193 99.6
62: (ns/day) (hour/ns)
62: Performance: 7.627 3.147
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.190 0.191 99.6
62: (ns/day) (hour/ns)
62: Performance: 7.708 3.114
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1392 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.198 0.198 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.412 3.238
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.230 0.232 99.1
62: (ns/day) (hour/ns)
62: Performance: 6.319 3.798
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.222 0.223 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.600 3.637
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.216 0.217 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.762 3.549
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.208 0.209 99.6
62: (ns/day) (hour/ns)
62: Performance: 7.025 3.416
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.209 0.209 99.6
62: (ns/day) (hour/ns)
62: Performance: 7.014 3.422
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1530 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.193 0.193 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.593 3.161
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.199 0.200 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.345 3.267
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.297 0.297 99.7
62: (ns/day) (hour/ns)
62: Performance: 4.939 4.860
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.262 0.263 99.7
62: (ns/day) (hour/ns)
62: Performance: 5.589 4.294
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.225 0.225 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.524 3.679
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.748 0.748 99.9
62: (ns/day) (hour/ns)
62: Performance: 1.963 12.228
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (2155 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.236 0.236 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.229 3.853
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.210 0.211 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.977 3.440
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.205 99.5
62: (ns/day) (hour/ns)
62: Performance: 7.164 3.350
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.211 0.212 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.937 3.460
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.213 0.213 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.889 3.484
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.199 0.199 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.377 3.253
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1509 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.228 0.228 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.436 3.729
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.226 0.226 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.489 3.699
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.225 0.226 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.492 3.697
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.207 0.208 99.6
62: (ns/day) (hour/ns)
62: Performance: 7.077 3.391
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.185 0.186 99.5
62: (ns/day) (hour/ns)
62: Performance: 7.902 3.037
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.240 0.241 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.092 3.939
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1534 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.193 0.193 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.597 3.159
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.214 0.217 98.9
62: (ns/day) (hour/ns)
62: Performance: 6.774 3.543
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.201 0.202 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.283 3.296
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.304 0.304 99.8
62: (ns/day) (hour/ns)
62: Performance: 4.830 4.969
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.192 0.192 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.644 3.140
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.221 0.222 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.624 3.623
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1553 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.198 0.198 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.426 3.232
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.232 0.232 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.323 3.795
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.274 0.275 99.7
62: (ns/day) (hour/ns)
62: Performance: 5.347 4.489
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.196 0.197 99.6
62: (ns/day) (hour/ns)
62: Performance: 7.466 3.215
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.264 0.265 99.7
62: (ns/day) (hour/ns)
62: Performance: 5.546 4.328
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.210 0.213 98.5
62: (ns/day) (hour/ns)
62: Performance: 6.881 3.488
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (1596 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.221 0.222 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.630 3.620
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.324 0.324 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.528 5.300
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.487 0.488 99.9
62: (ns/day) (hour/ns)
62: Performance: 3.012 7.967
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.309 0.309 99.8
62: (ns/day) (hour/ns)
62: Performance: 4.747 5.055
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.250 0.250 99.7
62: (ns/day) (hour/ns)
62: Performance: 5.866 4.091
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.268 0.269 99.7
62: (ns/day) (hour/ns)
62: Performance: 5.465 4.392
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (2084 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.212 0.212 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.921 3.468
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.348 0.348 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.221 5.686
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.212 0.213 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.911 3.473
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.206 0.206 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.120 3.371
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.197 0.197 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.452 3.221
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.263 0.263 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.579 4.302
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (1665 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.201 3.333
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.263 0.264 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.572 4.308
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.210 0.210 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.995 3.431
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.743 0.744 100.0
62: (ns/day) (hour/ns)
62: Performance: 1.975 12.149
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.326 0.327 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.496 5.338
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.218 0.218 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.742 3.560
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (2189 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.191 0.191 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.676 3.127
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.221 0.222 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.625 3.623
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.205 0.206 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.138 3.362
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.283 0.283 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.188 4.626
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.229 0.230 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.392 3.755
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.218 0.219 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.718 3.573
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (1578 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.257 0.258 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.699 4.211
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.210 0.210 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.979 3.439
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.613 0.613 99.9
62: (ns/day) (hour/ns)
62: Performance: 2.395 10.020
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.257 0.258 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.700 4.210
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 1.071 1.072 99.9
62: (ns/day) (hour/ns)
62: Performance: 1.370 17.515
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.207 0.208 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.071 3.394
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (2887 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.228 0.228 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.440 3.727
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.203 0.204 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.217 3.325
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.209 3.329
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.196 0.197 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.472 3.212
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.203 0.203 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.228 3.320
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.203 0.203 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.229 3.320
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (1482 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.186 0.186 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.882 3.045
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.207 0.207 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.083 3.388
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.203 0.203 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.219 3.325
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.201 0.202 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.269 3.301
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.194 0.195 99.6
62: (ns/day) (hour/ns)
62: Performance: 7.542 3.182
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.205 0.206 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.143 3.360
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (1442 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.190 0.190 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.729 3.105
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.197 0.197 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.438 3.227
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.216 0.216 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.789 3.535
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.194 0.195 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.548 3.180
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.196 0.196 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.480 3.208
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.196 0.196 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.489 3.205
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (1420 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.169 0.170 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.656 2.773
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.239 0.239 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.141 3.908
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.201 0.201 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.302 3.287
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.217 0.218 99.6
62: (ns/day) (hour/ns)
62: Performance: 6.739 3.562
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.185 0.186 99.6
62: (ns/day) (hour/ns)
62: Performance: 7.917 3.032
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.208 0.209 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.036 3.411
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (1445 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.191 0.191 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.675 3.127
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.197 0.198 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.429 3.231
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.219 0.220 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.689 3.588
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.6
62: (ns/day) (hour/ns)
62: Performance: 7.188 3.339
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.175 0.176 99.6
62: (ns/day) (hour/ns)
62: Performance: 8.356 2.872
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.189 0.190 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.732 3.104
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (1462 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.221 0.221 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.635 3.617
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.205 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.174 3.346
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.239 0.239 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.141 3.908
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.261 0.261 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.624 4.267
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.585 0.586 99.9
62: (ns/day) (hour/ns)
62: Performance: 2.508 9.568
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.406 0.406 99.9
62: (ns/day) (hour/ns)
62: Performance: 3.613 6.642
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (2165 ms)
62: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (42911 ms total)
62:
62: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.211 0.211 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.947 3.455
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.196 0.197 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.459 3.217
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.192 0.192 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.643 3.140
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.210 0.211 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.966 3.445
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.218 0.219 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.714 3.575
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.212 0.212 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.915 3.471
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (21807 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.187 0.187 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.842 3.061
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.198 0.199 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.386 3.249
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.227 0.229 99.0
62: (ns/day) (hour/ns)
62: Performance: 6.409 3.745
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.708 0.709 99.9
62: (ns/day) (hour/ns)
62: Performance: 2.072 11.583
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.241 0.242 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.078 3.949
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.227 0.228 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.451 3.721
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (23969 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.216 0.217 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.782 3.539
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.222 0.223 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.601 3.636
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.306 0.307 99.8
62: (ns/day) (hour/ns)
62: Performance: 4.786 5.015
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.205 99.6
62: (ns/day) (hour/ns)
62: Performance: 7.155 3.354
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.222 0.223 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.601 3.636
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.225 0.226 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.506 3.689
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (21510 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.239 0.239 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.145 3.906
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.247 0.247 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.940 4.040
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.212 0.213 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.903 3.477
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.233 0.234 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.285 3.819
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.193 0.193 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.595 3.160
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.222 0.222 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.607 3.632
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (20617 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.206 0.206 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.121 3.370
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.224 0.224 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.553 3.663
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.228 0.229 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.424 3.736
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.229 0.230 99.6
62: (ns/day) (hour/ns)
62: Performance: 6.398 3.751
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.210 0.211 99.4
62: (ns/day) (hour/ns)
62: Performance: 6.964 3.446
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.254 0.255 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.762 4.165
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (21534 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.226 0.226 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.493 3.696
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.246 0.247 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.954 4.031
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.224 0.225 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.542 3.669
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.222 0.223 99.6
62: (ns/day) (hour/ns)
62: Performance: 6.591 3.641
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.222 0.223 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.596 3.639
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.220 0.221 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.658 3.604
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (21285 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.219 0.219 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.713 3.575
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.223 0.223 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.588 3.643
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.226 0.227 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.472 3.708
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.224 0.225 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.534 3.673
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.227 0.228 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.444 3.724
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.178 0.178 99.7
62: (ns/day) (hour/ns)
62: Performance: 8.250 2.909
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (20551 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.240 0.240 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.117 3.924
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.225 0.225 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.521 3.680
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.225 0.225 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.514 3.685
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.217 0.218 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.748 3.557
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.224 0.225 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.542 3.668
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.215 0.216 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.809 3.525
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (20747 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.226 0.226 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.490 3.698
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.228 0.228 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.436 3.729
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.184 0.185 99.6
62: (ns/day) (hour/ns)
62: Performance: 7.943 3.021
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.208 0.209 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.034 3.412
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.220 0.220 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.673 3.597
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.226 0.227 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.474 3.707
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (21562 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.242 0.242 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.057 3.962
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.231 0.232 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.341 3.785
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.241 0.241 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.084 3.945
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.195 0.195 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.537 3.184
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.205 0.206 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.145 3.359
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.221 0.224 98.8
62: (ns/day) (hour/ns)
62: Performance: 6.553 3.663
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (22246 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.232 0.232 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.331 3.791
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.230 0.230 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.380 3.762
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.216 0.216 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.794 3.533
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.234 0.235 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.247 3.842
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.220 0.220 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.666 3.600
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.215 0.216 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.811 3.524
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (21617 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.240 0.240 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.123 3.919
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.206 3.331
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.221 0.221 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.638 3.615
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.215 0.216 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.814 3.522
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.241 0.242 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.080 3.947
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.252 0.253 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.811 4.130
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (21269 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.222 0.223 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.592 3.641
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.222 0.222 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.616 3.628
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.229 0.230 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.397 3.752
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.226 0.227 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.484 3.702
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.225 0.225 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.517 3.683
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.200 0.201 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.325 3.276
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (21530 ms)
62: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (280248 ms total)
62:
62: [----------] Global test environment tear-down
62: [==========] 39 tests from 3 test cases ran. (324807 ms total)
62: [ PASSED ] 39 tests.
62/65 Test #62: MdrunMpiCoordinationTestsOneRank ...... Passed 324.90 sec
test 63
Start 63: MdrunMpiCoordinationTestsTwoRanks
63: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsTwoRanks.xml"
63: Test timeout computed to be: 1920
63: [==========] Running 39 tests from 3 test cases.
63: [----------] Global test environment set-up.
63: [----------] 1 test from BasicPropagators/PeriodicActionsTest
63: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.452 0.227 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.483 3.702
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.402 0.201 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.296 3.290
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 1.106 0.554 199.7
63: (ns/day) (hour/ns)
63: Performance: 2.652 9.049
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.497 0.249 199.5
63: (ns/day) (hour/ns)
63: Performance: 5.893 4.073
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.383 0.192 199.3
63: (ns/day) (hour/ns)
63: Performance: 7.642 3.141
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.390 0.196 199.3
63: (ns/day) (hour/ns)
63: Performance: 7.499 3.200
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1848 ms)
63: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1849 ms total)
63:
63: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.399 0.200 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.357 3.262
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.362 0.182 199.5
63: (ns/day) (hour/ns)
63: Performance: 8.089 2.967
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.364 0.183 199.3
63: (ns/day) (hour/ns)
63: Performance: 8.037 2.986
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.387 0.194 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.576 3.168
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.390 0.196 199.3
63: (ns/day) (hour/ns)
63: Performance: 7.511 3.195
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.372 0.189 197.5
63: (ns/day) (hour/ns)
63: Performance: 7.790 3.081
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1378 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.378 0.189 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.759 3.093
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.405 0.203 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.229 3.320
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.467 0.234 199.4
63: (ns/day) (hour/ns)
63: Performance: 6.277 3.823
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.469 0.235 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.244 3.844
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.432 0.217 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.771 3.545
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.410 0.206 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.137 3.363
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1530 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.362 0.181 199.5
63: (ns/day) (hour/ns)
63: Performance: 8.103 2.962
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.414 0.208 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.075 3.392
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.384 0.193 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.611 3.153
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.429 0.215 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.831 3.514
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.392 0.197 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.455 3.219
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.384 0.193 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.614 3.152
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1425 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.395 0.198 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.427 3.231
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.369 0.185 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.944 3.021
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.429 0.215 199.2
63: (ns/day) (hour/ns)
63: Performance: 6.825 3.517
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.428 0.215 199.2
63: (ns/day) (hour/ns)
63: Performance: 6.834 3.512
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.455 0.228 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.440 3.727
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.418 0.210 199.3
63: (ns/day) (hour/ns)
63: Performance: 7.006 3.426
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1497 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.406 0.203 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.221 3.324
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.369 0.185 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.950 3.019
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.402 0.201 199.3
63: (ns/day) (hour/ns)
63: Performance: 7.290 3.292
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.451 0.228 197.8
63: (ns/day) (hour/ns)
63: Performance: 6.446 3.723
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.392 0.197 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.472 3.212
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.387 0.194 199.3
63: (ns/day) (hour/ns)
63: Performance: 7.572 3.169
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1455 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 1.050 0.526 199.8
63: (ns/day) (hour/ns)
63: Performance: 2.795 8.587
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.480 0.241 199.5
63: (ns/day) (hour/ns)
63: Performance: 6.106 3.931
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.381 0.191 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.685 3.123
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.406 0.204 199.3
63: (ns/day) (hour/ns)
63: Performance: 7.214 3.327
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.543 0.272 199.5
63: (ns/day) (hour/ns)
63: Performance: 5.397 4.447
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 1.495 0.748 199.8
63: (ns/day) (hour/ns)
63: Performance: 1.963 12.229
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (2434 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 1.107 0.554 199.8
63: (ns/day) (hour/ns)
63: Performance: 2.652 9.050
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.546 0.274 199.6
63: (ns/day) (hour/ns)
63: Performance: 5.366 4.472
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.607 0.304 199.5
63: (ns/day) (hour/ns)
63: Performance: 4.832 4.967
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.400 0.201 199.3
63: (ns/day) (hour/ns)
63: Performance: 7.324 3.277
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.380 0.191 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.695 3.119
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.359 0.180 199.3
63: (ns/day) (hour/ns)
63: Performance: 8.155 2.943
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1957 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.398 0.199 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.368 3.257
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.410 0.206 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.143 3.360
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.448 0.225 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.527 3.677
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.403 0.202 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.267 3.302
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.387 0.194 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.566 3.172
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.409 0.205 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.161 3.351
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1542 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.382 0.192 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.669 3.130
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.414 0.210 197.8
63: (ns/day) (hour/ns)
63: Performance: 7.008 3.425
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.398 0.200 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.360 3.261
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.428 0.215 199.4
63: (ns/day) (hour/ns)
63: Performance: 6.842 3.508
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.388 0.195 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.550 3.179
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.388 0.194 199.3
63: (ns/day) (hour/ns)
63: Performance: 7.553 3.178
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1443 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63:
63: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Using Berendsen pressure coupling invalidates the true ensemble for the
63: thermostat
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63:
63: There was 1 warning
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.403 0.202 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.268 3.302
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63:
63: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Using Berendsen pressure coupling invalidates the true ensemble for the
63: thermostat
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63:
63: There was 1 warning
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.427 0.214 199.5
63: (ns/day) (hour/ns)
63: Performance: 6.861 3.498
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63:
63: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Using Berendsen pressure coupling invalidates the true ensemble for the
63: thermostat
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63:
63: There was 1 warning
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.398 0.200 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.346 3.267
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63:
63: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Using Berendsen pressure coupling invalidates the true ensemble for the
63: thermostat
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63:
63: There was 1 warning
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.353 0.177 199.2
63: (ns/day) (hour/ns)
63: Performance: 8.287 2.896
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63:
63: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Using Berendsen pressure coupling invalidates the true ensemble for the
63: thermostat
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63:
63: There was 1 warning
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.379 0.190 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.719 3.109
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63:
63: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Using Berendsen pressure coupling invalidates the true ensemble for the
63: thermostat
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63:
63: There was 1 warning
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 1.492 0.747 199.8
63: (ns/day) (hour/ns)
63: Performance: 1.966 12.206
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1988 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.538 0.269 199.7
63: (ns/day) (hour/ns)
63: Performance: 5.455 4.400
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.435 0.218 199.5
63: (ns/day) (hour/ns)
63: Performance: 6.732 3.565
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.383 0.192 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.636 3.143
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.409 0.207 197.9
63: (ns/day) (hour/ns)
63: Performance: 7.099 3.381
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.426 0.214 199.1
63: (ns/day) (hour/ns)
63: Performance: 6.859 3.499
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.380 0.191 199.1
63: (ns/day) (hour/ns)
63: Performance: 7.696 3.118
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1533 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.404 0.202 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.258 3.307
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.365 0.183 199.3
63: (ns/day) (hour/ns)
63: Performance: 8.030 2.989
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.402 0.202 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.285 3.295
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.494 0.248 199.2
63: (ns/day) (hour/ns)
63: Performance: 5.924 4.051
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.475 0.239 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.156 3.899
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.386 0.194 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.572 3.170
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1510 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.404 0.203 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.251 3.310
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.391 0.196 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.503 3.199
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.429 0.215 199.5
63: (ns/day) (hour/ns)
63: Performance: 6.825 3.517
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.429 0.215 199.4
63: (ns/day) (hour/ns)
63: Performance: 6.828 3.515
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.410 0.205 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.149 3.357
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.364 0.183 199.4
63: (ns/day) (hour/ns)
63: Performance: 8.036 2.986
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1456 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.422 0.211 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.953 3.452
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.407 0.204 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.196 3.335
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.421 0.211 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.950 3.453
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.378 0.190 199.1
63: (ns/day) (hour/ns)
63: Performance: 7.737 3.102
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.393 0.197 199.3
63: (ns/day) (hour/ns)
63: Performance: 7.452 3.220
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 1.460 0.731 199.8
63: (ns/day) (hour/ns)
63: Performance: 2.010 11.940
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (1997 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.524 0.262 199.7
63: (ns/day) (hour/ns)
63: Performance: 5.603 4.284
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 1.230 0.616 199.8
63: (ns/day) (hour/ns)
63: Performance: 2.386 10.060
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.553 0.277 199.3
63: (ns/day) (hour/ns)
63: Performance: 5.294 4.534
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.432 0.217 199.1
63: (ns/day) (hour/ns)
63: Performance: 6.766 3.547
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.455 0.228 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.430 3.733
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.482 0.242 199.4
63: (ns/day) (hour/ns)
63: Performance: 6.078 3.949
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (2085 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.378 0.190 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.741 3.100
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.379 0.190 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.722 3.108
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.406 0.204 199.3
63: (ns/day) (hour/ns)
63: Performance: 7.214 3.327
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.421 0.212 199.1
63: (ns/day) (hour/ns)
63: Performance: 6.940 3.458
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.402 0.202 199.3
63: (ns/day) (hour/ns)
63: Performance: 7.289 3.293
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.447 0.224 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.547 3.666
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (1483 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.376 0.189 199.1
63: (ns/day) (hour/ns)
63: Performance: 7.769 3.089
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.390 0.196 199.1
63: (ns/day) (hour/ns)
63: Performance: 7.502 3.199
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.451 0.226 199.2
63: (ns/day) (hour/ns)
63: Performance: 6.490 3.698
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.492 0.247 199.3
63: (ns/day) (hour/ns)
63: Performance: 5.948 4.035
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.500 0.251 199.3
63: (ns/day) (hour/ns)
63: Performance: 5.851 4.102
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.545 0.273 199.4
63: (ns/day) (hour/ns)
63: Performance: 5.373 4.467
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (1621 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.384 0.194 197.7
63: (ns/day) (hour/ns)
63: Performance: 7.553 3.177
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.408 0.205 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.177 3.344
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.420 0.211 199.2
63: (ns/day) (hour/ns)
63: Performance: 6.960 3.448
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 2.920 1.461 199.9
63: (ns/day) (hour/ns)
63: Performance: 1.005 23.869
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.433 0.217 199.2
63: (ns/day) (hour/ns)
63: Performance: 6.754 3.553
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.549 0.275 199.4
63: (ns/day) (hour/ns)
63: Performance: 5.334 4.499
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (2799 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.384 0.193 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.629 3.146
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.372 0.186 199.3
63: (ns/day) (hour/ns)
63: Performance: 7.880 3.046
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.368 0.185 199.1
63: (ns/day) (hour/ns)
63: Performance: 7.939 3.023
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.392 0.197 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.471 3.212
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.371 0.186 199.0
63: (ns/day) (hour/ns)
63: Performance: 7.881 3.045
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.371 0.186 199.1
63: (ns/day) (hour/ns)
63: Performance: 7.882 3.045
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (1355 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.592 0.297 199.5
63: (ns/day) (hour/ns)
63: Performance: 4.951 4.848
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 1.361 0.682 199.7
63: (ns/day) (hour/ns)
63: Performance: 2.155 11.137
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.473 0.238 199.2
63: (ns/day) (hour/ns)
63: Performance: 6.183 3.882
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.393 0.198 199.0
63: (ns/day) (hour/ns)
63: Performance: 7.437 3.227
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.416 0.209 199.1
63: (ns/day) (hour/ns)
63: Performance: 7.024 3.417
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.418 0.210 199.1
63: (ns/day) (hour/ns)
63: Performance: 7.003 3.427
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (2044 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.410 0.205 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.152 3.356
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.397 0.199 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.384 3.250
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.391 0.196 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.477 3.210
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.407 0.204 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.195 3.336
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.389 0.195 199.1
63: (ns/day) (hour/ns)
63: Performance: 7.524 3.190
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.412 0.207 199.1
63: (ns/day) (hour/ns)
63: Performance: 7.106 3.377
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (1433 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.387 0.194 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.573 3.169
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.440 0.220 199.5
63: (ns/day) (hour/ns)
63: Performance: 6.662 3.602
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.391 0.196 199.1
63: (ns/day) (hour/ns)
63: Performance: 7.488 3.205
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.367 0.184 199.1
63: (ns/day) (hour/ns)
63: Performance: 7.971 3.011
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.460 0.231 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.361 3.773
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.459 0.230 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.383 3.760
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (1478 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 1.211 0.606 199.9
63: (ns/day) (hour/ns)
63: Performance: 2.425 9.898
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.371 0.186 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.888 3.042
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.388 0.195 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.545 3.181
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.414 0.208 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.075 3.392
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.392 0.197 199.1
63: (ns/day) (hour/ns)
63: Performance: 7.457 3.218
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.371 0.186 199.1
63: (ns/day) (hour/ns)
63: Performance: 7.884 3.044
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (1800 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.389 0.195 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.538 3.184
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.455 0.228 199.5
63: (ns/day) (hour/ns)
63: Performance: 6.437 3.728
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.414 0.208 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.072 3.394
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.390 0.196 199.1
63: (ns/day) (hour/ns)
63: Performance: 7.490 3.204
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.438 0.220 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.690 3.588
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.545 0.273 199.4
63: (ns/day) (hour/ns)
63: Performance: 5.373 4.467
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (1548 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.452 0.227 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.485 3.701
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.392 0.196 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.476 3.210
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.413 0.207 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.079 3.390
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.436 0.219 199.2
63: (ns/day) (hour/ns)
63: Performance: 6.716 3.573
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.393 0.197 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.441 3.226
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 1.438 0.720 199.8
63: (ns/day) (hour/ns)
63: Performance: 2.040 11.764
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (1997 ms)
63: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (42794 ms total)
63:
63: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.467 0.234 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.284 3.819
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.473 0.237 199.5
63: (ns/day) (hour/ns)
63: Performance: 6.193 3.875
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.419 0.210 199.1
63: (ns/day) (hour/ns)
63: Performance: 6.985 3.436
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.447 0.226 197.7
63: (ns/day) (hour/ns)
63: Performance: 6.490 3.698
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.416 0.209 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.034 3.412
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.554 0.278 199.4
63: (ns/day) (hour/ns)
63: Performance: 5.286 4.540
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (23567 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.392 0.196 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.483 3.207
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.421 0.211 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.953 3.452
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.448 0.225 199.2
63: (ns/day) (hour/ns)
63: Performance: 6.536 3.672
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.408 0.205 199.1
63: (ns/day) (hour/ns)
63: Performance: 7.171 3.347
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.436 0.219 199.2
63: (ns/day) (hour/ns)
63: Performance: 6.712 3.576
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.552 0.277 199.2
63: (ns/day) (hour/ns)
63: Performance: 5.305 4.524
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (20595 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.456 0.228 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.434 3.730
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.457 0.229 199.2
63: (ns/day) (hour/ns)
63: Performance: 6.408 3.745
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.421 0.212 199.2
63: (ns/day) (hour/ns)
63: Performance: 6.944 3.456
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.418 0.210 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.000 3.428
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.404 0.203 198.9
63: (ns/day) (hour/ns)
63: Performance: 7.232 3.319
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.402 0.202 198.9
63: (ns/day) (hour/ns)
63: Performance: 7.260 3.306
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (22121 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.406 0.203 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.218 3.325
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.416 0.209 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.028 3.415
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.436 0.219 199.0
63: (ns/day) (hour/ns)
63: Performance: 6.702 3.581
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.435 0.218 199.4
63: (ns/day) (hour/ns)
63: Performance: 6.729 3.567
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.408 0.205 199.3
63: (ns/day) (hour/ns)
63: Performance: 7.171 3.347
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.441 0.221 199.4
63: (ns/day) (hour/ns)
63: Performance: 6.645 3.612
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (22131 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.424 0.213 199.5
63: (ns/day) (hour/ns)
63: Performance: 6.907 3.475
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.450 0.225 199.5
63: (ns/day) (hour/ns)
63: Performance: 6.517 3.683
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.433 0.218 198.6
63: (ns/day) (hour/ns)
63: Performance: 6.744 3.558
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.441 0.221 199.4
63: (ns/day) (hour/ns)
63: Performance: 6.641 3.614
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.425 0.213 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.885 3.486
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.429 0.215 199.4
63: (ns/day) (hour/ns)
63: Performance: 6.824 3.517
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (21721 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.455 0.228 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.446 3.723
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.443 0.222 199.4
63: (ns/day) (hour/ns)
63: Performance: 6.605 3.633
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.497 0.250 199.3
63: (ns/day) (hour/ns)
63: Performance: 5.883 4.079
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.435 0.218 199.2
63: (ns/day) (hour/ns)
63: Performance: 6.728 3.567
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.428 0.215 199.1
63: (ns/day) (hour/ns)
63: Performance: 6.831 3.513
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.439 0.220 199.2
63: (ns/day) (hour/ns)
63: Performance: 6.665 3.601
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (21977 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.459 0.230 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.393 3.754
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.428 0.215 199.4
63: (ns/day) (hour/ns)
63: Performance: 6.842 3.508
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.440 0.221 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.658 3.604
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.441 0.221 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.634 3.618
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.430 0.216 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.803 3.528
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.497 0.249 199.4
63: (ns/day) (hour/ns)
63: Performance: 5.890 4.075
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (22234 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.438 0.219 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.701 3.582
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.486 0.244 199.4
63: (ns/day) (hour/ns)
63: Performance: 6.025 3.983
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.491 0.247 199.2
63: (ns/day) (hour/ns)
63: Performance: 5.956 4.030
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.450 0.226 199.1
63: (ns/day) (hour/ns)
63: Performance: 6.498 3.694
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.428 0.215 199.2
63: (ns/day) (hour/ns)
63: Performance: 6.830 3.514
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.433 0.217 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.763 3.549
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (21632 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.443 0.222 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.615 3.628
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.398 0.199 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.368 3.257
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.488 0.245 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.003 3.998
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.458 0.230 199.2
63: (ns/day) (hour/ns)
63: Performance: 6.389 3.756
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.390 0.196 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.502 3.199
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.458 0.230 199.1
63: (ns/day) (hour/ns)
63: Performance: 6.392 3.754
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (22223 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.449 0.225 199.2
63: (ns/day) (hour/ns)
63: Performance: 6.522 3.680
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.436 0.219 199.1
63: (ns/day) (hour/ns)
63: Performance: 6.708 3.578
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.472 0.237 199.1
63: (ns/day) (hour/ns)
63: Performance: 6.197 3.873
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.425 0.214 198.7
63: (ns/day) (hour/ns)
63: Performance: 6.874 3.492
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.453 0.228 198.5
63: (ns/day) (hour/ns)
63: Performance: 6.432 3.731
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.458 0.230 199.1
63: (ns/day) (hour/ns)
63: Performance: 6.387 3.757
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (21361 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.410 0.206 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.146 3.358
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.493 0.247 199.5
63: (ns/day) (hour/ns)
63: Performance: 5.943 4.038
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.457 0.229 199.3
63: (ns/day) (hour/ns)
63: Performance: 6.409 3.745
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.414 0.208 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.063 3.398
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.422 0.212 199.2
63: (ns/day) (hour/ns)
63: Performance: 6.931 3.463
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.405 0.203 199.1
63: (ns/day) (hour/ns)
63: Performance: 7.227 3.321
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (22035 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.446 0.224 199.0
63: (ns/day) (hour/ns)
63: Performance: 6.547 3.666
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.435 0.219 198.9
63: (ns/day) (hour/ns)
63: Performance: 6.721 3.571
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.449 0.226 198.9
63: (ns/day) (hour/ns)
63: Performance: 6.512 3.685
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.476 0.239 198.9
63: (ns/day) (hour/ns)
63: Performance: 6.133 3.913
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.480 0.242 198.9
63: (ns/day) (hour/ns)
63: Performance: 6.082 3.946
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.458 0.230 198.9
63: (ns/day) (hour/ns)
63: Performance: 6.385 3.759
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (22350 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.399 0.200 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.347 3.266
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.404 0.203 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.242 3.314
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.436 0.220 197.9
63: (ns/day) (hour/ns)
63: Performance: 6.668 3.599
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.425 0.214 199.2
63: (ns/day) (hour/ns)
63: Performance: 6.878 3.489
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.426 0.214 199.1
63: (ns/day) (hour/ns)
63: Performance: 6.862 3.498
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.493 0.247 199.3
63: (ns/day) (hour/ns)
63: Performance: 5.945 4.037
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (21310 ms)
63: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (285260 ms total)
63:
63: [----------] Global test environment tear-down
63: [==========] 39 tests from 3 test cases ran. (330012 ms total)
63: [ PASSED ] 39 tests.
63/65 Test #63: MdrunMpiCoordinationTestsTwoRanks ..... Passed 330.12 sec
test 64
Start 64: MdrunFEPTests
64: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunfep-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunFEPTests.xml"
64: Test timeout computed to be: 600
64: [==========] Running 10 tests from 1 test case.
64: [----------] Global test environment set-up.
64: [----------] 10 tests from FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]:
64: For proper sampling of the (nearly) decoupled state, stochastic dynamics
64: should be used
64:
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 4 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to -1277178133
64:
64: Generated 153 of the 153 non-bonded parameter combinations
64:
64: Generated 153 of the 153 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64:
64: Coupling 1 copies of molecule type 'ASN'
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 1.168 0.585 199.9
64: (ns/day) (hour/ns)
64: Performance: 3.104 7.732
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision)
64: [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (10841 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]:
64: For proper sampling of the (nearly) decoupled state, stochastic dynamics
64: should be used
64:
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 4 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to -16908553
64:
64: Generated 153 of the 153 non-bonded parameter combinations
64:
64: Generated 153 of the 153 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64:
64: Coupling 1 copies of molecule type 'ASN'
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 1.113 0.557 199.9
64: (ns/day) (hour/ns)
64: Performance: 3.258 7.367
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (800 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]:
64: For proper sampling of the (nearly) decoupled state, stochastic dynamics
64: should be used
64:
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]:
64: With PME there is a minor soft core effect present at the cut-off,
64: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
64: energy conservation, but usually other effects dominate. With a common
64: sigma value of 0.34 nm the fraction of the particle-particle potential at
64: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06.
64:
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 5 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 5 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to 2133703897
64:
64: Generated 153 of the 153 non-bonded parameter combinations
64:
64: Generated 153 of the 153 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64:
64: Coupling 1 copies of molecule type 'ASN'
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 1.326 0.663 199.9
64: (ns/day) (hour/ns)
64: Performance: 2.735 8.776
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (903 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]:
64: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off
64: and vdw_modifier=Force-switch
64:
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 4 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 100 steps, 0.1 ps.
64: Setting the LD random seed to -16834716
64:
64: Generated 153 of the 153 non-bonded parameter combinations
64:
64: Generated 153 of the 153 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64:
64: Coupling 1 copies of molecule type 'ASN'
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 3.766 1.884 200.0
64: (ns/day) (hour/ns)
64: Performance: 4.633 5.180
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Reading energy frame 30 time 0.030
Reading energy frame 40 time 0.040
Reading energy frame 50 time 0.050
Reading energy frame 60 time 0.060
Reading energy frame 70 time 0.070
Reading energy frame 80 time 0.080
Reading energy frame 90 time 0.090
Reading energy frame 100 time 0.100
Last energy frame read 100 time 0.100 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (2094 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64:
64: WARNING 1 [file topol.top, line 72]:
64: No default Bond types for perturbed atoms, using normal values
64:
64:
64: WARNING 2 [file topol.top, line 73]:
64: No default Bond types for perturbed atoms, using normal values
64:
64:
64: WARNING 3 [file topol.top, line 98]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 4 [file topol.top, line 99]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 5 [file topol.top, line 100]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 6 [file topol.top, line 101]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 7 [file topol.top, line 111]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64:
64: WARNING 8 [file topol.top, line 112]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64:
64: WARNING 9 [file topol.top, line 113]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64:
64: WARNING 10 [file topol.top, line 114]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 3 notes
64:
64: There were 10 warnings
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to -26616461
64:
64: Generated 136 of the 136 non-bonded parameter combinations
64:
64: Generated 136 of the 136 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 1.371 0.686 199.9
64: (ns/day) (hour/ns)
64: Performance: 2.644 9.076
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (928 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64:
64: WARNING 1 [file topol.top, line 72]:
64: No default Bond types for perturbed atoms, using normal values
64:
64:
64: WARNING 2 [file topol.top, line 73]:
64: No default Bond types for perturbed atoms, using normal values
64:
64:
64: WARNING 3 [file topol.top, line 98]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 4 [file topol.top, line 99]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 5 [file topol.top, line 100]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 6 [file topol.top, line 101]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 7 [file topol.top, line 111]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64:
64: WARNING 8 [file topol.top, line 112]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64:
64: WARNING 9 [file topol.top, line 113]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64:
64: WARNING 10 [file topol.top, line 114]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 3 notes
64:
64: There were 10 warnings
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to -33554437
64:
64: Generated 136 of the 136 non-bonded parameter combinations
64:
64: Generated 136 of the 136 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 1.491 0.746 199.9
64: (ns/day) (hour/ns)
64: Performance: 2.433 9.866
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (1002 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 3 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to -674256537
64:
64: Generated 136 of the 136 non-bonded parameter combinations
64:
64: Generated 136 of the 136 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.81
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 0.812 0.406 199.8
64: (ns/day) (hour/ns)
64: Performance: 4.465 5.375
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (579 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: There were 2 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to -205530145
64:
64: Generated 136 of the 136 non-bonded parameter combinations
64:
64: Generated 136 of the 136 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.81
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 1.005 0.503 199.8
64: (ns/day) (hour/ns)
64: Performance: 3.606 6.655
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (689 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]:
64: With PME there is a minor soft core effect present at the cut-off,
64: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
64: energy conservation, but usually other effects dominate. With a common
64: sigma value of 0.34 nm the fraction of the particle-particle potential at
64: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06.
64:
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 4 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: Setting the LD random seed to -103318533
64:
64: Generated 136 of the 136 non-bonded parameter combinations
64:
64: Generated 136 of the 136 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 1.178 0.589 199.9
64: (ns/day) (hour/ns)
64: Performance: 3.079 7.795
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (776 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]:
64: With PME there is a minor soft core effect present at the cut-off,
64: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
64: energy conservation, but usually other effects dominate. With a common
64: sigma value of 0.34 nm the fraction of the particle-particle potential at
64: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06.
64:
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 4 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: Setting the LD random seed to -893395457
64:
64: Generated 136 of the 136 non-bonded parameter combinations
64:
64: Generated 136 of the 136 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.81
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 1.037 0.519 199.9
64: (ns/day) (hour/ns)
64: Performance: 3.498 6.861
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (714 ms)
64: [----------] 10 tests from FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest (19343 ms total)
64:
64: [----------] Global test environment tear-down
64: [==========] 10 tests from 1 test case ran. (19382 ms total)
64: [ PASSED ] 10 tests.
64/65 Test #64: MdrunFEPTests ......................... Passed 19.45 sec
test 65
Start 65: MdrunSimulatorComparison
65: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunSimulatorComparison.xml"
65: Test timeout computed to be: 600
65: [==========] Running 0 tests from 0 test cases.
65: [==========] 0 tests from 0 test cases ran. (0 ms total)
65: [ PASSED ] 0 tests.
65:
65: YOU HAVE 18 DISABLED TESTS
65:
65/65 Test #65: MdrunSimulatorComparison .............. Passed 0.07 sec
100% tests passed, 0 tests failed out of 65
Label Time Summary:
GTest = 1405.69 sec*proc (63 tests)
IntegrationTest = 510.19 sec*proc (16 tests)
MpiTest = 889.73 sec*proc (8 tests)
SlowTest = 881.03 sec*proc (8 tests)
UnitTest = 14.47 sec*proc (39 tests)
Total Test time (real) = 1407.05 sec
/usr/bin/make -j4 -C build/basic-dp tests
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/make -f CMakeFiles/Makefile2 tests
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles 97
/usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
/usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/depend
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googletest /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock/gtest /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock/gtest && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -Dgtest_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googletest/include -I/<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -Wshadow -Werror -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=c++17 -MD -MT src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-all.cc
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build
Consolidate compiler generated dependencies of target mdrun_objlib
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3.9 -D HAVE_FULL_FUNCTIONING_PYTHON=Python3_Interpreter_FOUND -D PROJECT_VERSION=2021.3-Raspbian-2021.3-4 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2021.3-4 -D SOURCE_IS_SOURCE_DISTRIBUTION=ON -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoWithoutGit.cmake
Consolidate compiler generated dependencies of target scanner
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 0%] Built target mdrun_objlib
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
[ 0%] Built target scanner
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
[ 0%] Built target release-version-info
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
Consolidate compiler generated dependencies of target lmfit_objlib
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 0%] Built target lmfit_objlib
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
Consolidate compiler generated dependencies of target tng_io_obj
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 2%] Built target tng_io_obj
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
Consolidate compiler generated dependencies of target linearalgebra
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
Consolidate compiler generated dependencies of target thread_mpi
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build
[ 2%] Built target linearalgebra
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 4%] Built target thread_mpi
Consolidate compiler generated dependencies of target modularsimulator
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 5%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Consolidate compiler generated dependencies of target libgromacs
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 62%] Built target libgromacs
/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake --color=
Consolidate compiler generated dependencies of target nblib
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 63%] Built target nblib
/usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend
/usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/samples /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/samples /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake --color=
Consolidate compiler generated dependencies of target methane-water-integration
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
Consolidate compiler generated dependencies of target argon-forces-integration
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 64%] Built target methane-water-integration
[ 65%] Built target argon-forces-integration
cd /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock/gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so -o ../../../../../lib/libgtest.so CMakeFiles/gtest.dir/src/gtest-all.cc.o -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 65%] Built target gtest
/usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -Wshadow -Werror -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++17 -MD -MT src/external/googletest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o -MF CMakeFiles/gmock.dir/src/gmock-all.cc.o.d -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googlemock/src/gmock-all.cc
cd /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so -o ../../../../lib/libgmock.so CMakeFiles/gmock.dir/src/gmock-all.cc.o ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 65%] Built target gmock
/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/testutils /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/cmdlinetest.cpp.o -MF CMakeFiles/testutils.dir/cmdlinetest.cpp.o.d -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/cmdlinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/conftest.cpp.o -MF CMakeFiles/testutils.dir/conftest.cpp.o.d -o CMakeFiles/testutils.dir/conftest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/conftest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/filematchers.cpp.o -MF CMakeFiles/testutils.dir/filematchers.cpp.o.d -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/filematchers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/interactivetest.cpp.o -MF CMakeFiles/testutils.dir/interactivetest.cpp.o.d -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/interactivetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/loggertest.cpp.o -MF CMakeFiles/testutils.dir/loggertest.cpp.o.d -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/loggertest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/mpi_printer.cpp.o -MF CMakeFiles/testutils.dir/mpi_printer.cpp.o.d -o CMakeFiles/testutils.dir/mpi_printer.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpi_printer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/mpitest.cpp.o -MF CMakeFiles/testutils.dir/mpitest.cpp.o.d -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/refdata.cpp.o -MF CMakeFiles/testutils.dir/refdata.cpp.o.d -o CMakeFiles/testutils.dir/refdata.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/refdata_xml.cpp.o -MF CMakeFiles/testutils.dir/refdata_xml.cpp.o.d -o CMakeFiles/testutils.dir/refdata_xml.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata_xml.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/simulationdatabase.cpp.o -MF CMakeFiles/testutils.dir/simulationdatabase.cpp.o.d -o CMakeFiles/testutils.dir/simulationdatabase.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/simulationdatabase.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/stdiohelper.cpp.o -MF CMakeFiles/testutils.dir/stdiohelper.cpp.o.d -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stdiohelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/stringtest.cpp.o -MF CMakeFiles/testutils.dir/stringtest.cpp.o.d -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stringtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/testasserts.cpp.o -MF CMakeFiles/testutils.dir/testasserts.cpp.o.d -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testasserts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/testfilemanager.cpp.o -MF CMakeFiles/testutils.dir/testfilemanager.cpp.o.d -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfilemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/testfileredirector.cpp.o -MF CMakeFiles/testutils.dir/testfileredirector.cpp.o.d -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/test_device.cpp.o -MF CMakeFiles/testutils.dir/test_device.cpp.o.d -o CMakeFiles/testutils.dir/test_device.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/test_device.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/test_hardware_environment.cpp.o -MF CMakeFiles/testutils.dir/test_hardware_environment.cpp.o.d -o CMakeFiles/testutils.dir/test_hardware_environment.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/test_hardware_environment.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/testinit.cpp.o -MF CMakeFiles/testutils.dir/testinit.cpp.o.d -o CMakeFiles/testutils.dir/testinit.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testinit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/testmatchers.cpp.o -MF CMakeFiles/testutils.dir/testmatchers.cpp.o.d -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testmatchers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/testoptions.cpp.o -MF CMakeFiles/testutils.dir/testoptions.cpp.o.d -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/textblockmatchers.cpp.o -MF CMakeFiles/testutils.dir/textblockmatchers.cpp.o.d -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/textblockmatchers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -MF CMakeFiles/testutils.dir/tprfilegenerator.cpp.o.d -o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tprfilegenerator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/xvgtest.cpp.o -MF CMakeFiles/testutils.dir/xvgtest.cpp.o.d -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/xvgtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -MF CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o.d -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /<<PKGBUILDDIR>>/src/external/tinyxml2/tinyxml2.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1
/usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi_printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata_xml.cpp.o CMakeFiles/testutils.dir/simulationdatabase.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/test_device.cpp.o CMakeFiles/testutils.dir/test_hardware_environment.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o
/usr/bin/ranlib ../../lib/libtestutils.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 68%] Built target testutils
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/depend
/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/depend
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/testhelpers.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/testhelpers.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/testhelpers.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/testhelpers.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/mpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/interactivetest.cpp.o -MF CMakeFiles/testutils-test.dir/interactivetest.cpp.o.d -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/interactivetest.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energyreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/testsystems.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -MF CMakeFiles/testutils-test.dir/refdata_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.6.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 68%] Built target testutils-mpi-test
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -MF CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 68%] Built target utility-mpi-test
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/alignedallocator.cpp.o -MF CMakeFiles/utility-test.dir/alignedallocator.cpp.o.d -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testhelpers.cpp.o CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o
/usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 68%] Built target nblib_test_infrastructure
/usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -MF CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o.d -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulatorcomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/terminationhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -MF CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/arrayref.cpp.o -MF CMakeFiles/utility-test.dir/arrayref.cpp.o.d -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_SingleConstraint_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:315:51: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
315 | std::vector<real> masses = { 1.0, 12.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:317:45: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
317 | std::vector<real> constraintsR0 = { 0.1 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_TwoDisjointConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:376:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
376 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:380:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
380 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:382:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
382 | std::vector<RVec> v = { { 0.0, 1.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 0.0, 0.0, 1.0 }, { 0.0, 0.0, 0.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_ThreeSequentialConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:430:50: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
430 | std::vector<real> constraintsR0 = { 0.1, 0.2 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_ThreeConstraintsWithCentralAtom_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:494:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
494 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:499:59: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
499 | { -0.005, 0.011, 0.102 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:501:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
501 | std::vector<RVec> v = { { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_FourSequentialConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:554:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
554 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:558:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
558 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:560:106: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
560 | std::vector<RVec> v = { { 0.0, 0.0, 2.0 }, { 0.0, 0.0, 3.0 }, { 0.0, 0.0, -4.0 }, { 0.0, 0.0, -1.0 } };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.6.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 68%] Built target testutils-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
/<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp: In function 'bool gmx::test::shouldDoComparison(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::test::ComparisonConditions)':
/<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp:282:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
282 | static bool shouldDoComparison(ArrayRef<const RVec> values, ComparisonConditions comparisonConditions)
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::test::ConstraintsTestData::ConstraintsTestData(const string&, int, std::vector<double>, std::vector<int>, std::vector<double>, bool, real (*)[3], bool, float, real, real, const std::vector<gmx::BasicVector<double> >&, const std::vector<gmx::BasicVector<double> >&, const std::vector<gmx::BasicVector<double> >&, real, gmx_bool, int, int, real)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectoryreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target mdrun_test_infrastructure
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask64.cpp.o -MF CMakeFiles/utility-test.dir/bitmask64.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp: In member function 'virtual void gmx::test::ShakeConstraintsRunner::applyConstraints(gmx::test::ConstraintsTestData*, t_pbc)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp:87:35: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
87 | bool success = constrain_shake(
| ~~~~~~~~~~~~~~~^
88 | nullptr, &shaked, testData->invmass_.data(), *testData->idef_, testData->ir_, testData->x_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
89 | testData->xPrime_, testData->xPrime2_, nullptr, &testData->nrnb_, testData->lambda_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
90 | &testData->dHdLambda_, testData->invdt_, testData->v_, testData->computeVirial_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
91 | testData->virialScaled_, false, gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp:87:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp:87:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp:87:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp: In member function 'virtual void gmx::test::LincsConstraintsRunner::applyConstraints(gmx::test::ConstraintsTestData*, t_pbc)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp:127:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
127 | bool success = constrain_lincs(
| ~~~~~~~~~~~~~~~^
128 | false, testData->ir_, 0, lincsd, testData->invmass_.data(), &cr, &ms,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
129 | testData->x_.arrayRefWithPadding(), testData->xPrime_.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
130 | testData->xPrime2_.arrayRefWithPadding().unpaddedArrayRef(), pbc.box, &pbc,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
131 | testData->hasMassPerturbed_, testData->lambda_, &testData->dHdLambda_, testData->invdt_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
132 | testData->v_.arrayRefWithPadding().unpaddedArrayRef(), testData->computeVirial_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
133 | testData->virialScaled_, gmx::ConstraintVariable::Positions, &testData->nrnb_, maxwarn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
134 | &warncount_lincs);
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp:127:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energydrifttracker.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/expanded.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:235:80: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
235 | nullptr, step, step, seed_, nullptr);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:235:80: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:235:80: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp: In member function 'virtual void gmx::test::BiasTest_DetectsCovering_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:320:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
320 | nullptr, step, step, params.awhParams.seed, nullptr);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:320:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:320:88: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasgrid.cpp.o -MF CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasgrid.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/dimparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.h:61,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasgrid.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::test::biasGridTest_neighborhood_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/freeenergyparameters.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasstate.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:41:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::BiasFepLambdaStateTest::BiasFepLambdaStateTest()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/defaultinitializationallocator.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp: In member function 'virtual void gmx::test::BiasFepLambdaStateTest_ForcesBiasPmf_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:229:74: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | nullptr, nullptr, step * mdTimeStep, step, seed_, nullptr);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:229:74: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:229:74: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:41:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:41:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::test::BiasFepLambdaStateTest_DetectsCovering_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:309:67: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
309 | params.awhParams.seed, nullptr);
| ^
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:309:67: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:309:67: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
/usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -MF CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o.d -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/enumerationhelpers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasgrid.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.6.0.0 ../../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target awh-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/fixedcapacityvector.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_grp_tcstat&}; _Tp = t_grp_tcstat; _Alloc = std::allocator<t_grp_tcstat>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_grp_tcstat>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::test::LeapFrogTestData::LeapFrogTestData(int, real, const real*, const real*, int, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::test::LeapFrogHostTestRunner::integrate(gmx::test::LeapFrogTestData*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'static void gmx::test::{anonymous}::ElectricFieldTest::test(int, real, real, real, real, real)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/listoflists.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::test::SettleTestData::SettleTestData(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.6.0.0 ../../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestrunners.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target density_fitting_applied_forces-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target applied_forces-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o -MF CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o.d -o CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mdmodulenotification-impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::BasicVector<double>}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx::BasicVector<double> > gmx::{anonymous}::computeDisplacements(gmx::ArrayRef<const int>, const std::vector<gmx::BasicVector<double> >&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/mutex.cpp.o -MF CMakeFiles/utility-test.dir/mutex.cpp.o.d -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest::SetUp()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'static void gmx::{anonymous}::ShakeTest::runTest(size_t, size_t, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<gmx::BasicVector<double> >&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
198 | cshake(iatom.data(), numConstraints, &numIterations, ShakeTest::maxNumIterations_,
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
199 | constrainedDistancesSquared, finalPositions, nullptr, initialDisplacements,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | halfOfReducedMasses, omega_, inverseMasses.data(), distanceSquaredTolerances,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | lagrangianValues, &numErrors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:37:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsThreeBondsWithCommonAtoms_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoBondsWithACommonAtom_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoDisjointBonds_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsOneBond_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::test::{anonymous}::iListInput; _Alloc = std::allocator<gmx::test::{anonymous}::iListInput>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:63,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:56:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<typename testing::internal::IteratorTraits<Iterator>::value_type> testing::ValuesIn(ForwardIterator, ForwardIterator) [with ForwardIterator = __gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >]':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:304:1: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
304 | ValuesIn(ForwardIterator begin, ForwardIterator end) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:304:1: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_BondZeroLengthListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_PolarizeListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_BondListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_AngleListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_DihedralListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_RestraintsListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_AngleZeroListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >' changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o
/usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target onlinehelp-test-shared
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/path.cpp.o -MF CMakeFiles/utility-test.dir/path.cpp.o.d -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::PaddedVector<T, Allocator>::PaddedVector(const std::initializer_list<_Tp>&) [with T = gmx::BasicVector<double>; Allocator = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:646:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
646 | std::vector<iListInput> c_InputBonds = {
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:661:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
661 | std::vector<iListInput> c_InputAngles = {
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:685:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
685 | std::vector<iListInput> c_InputDihs = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:695:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
695 | std::vector<iListInput> c_InputPols = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:705:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
705 | std::vector<iListInput> c_InputRestraints = {
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:715:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
715 | std::vector<iListInput> c_InputBondsZeroLength = {
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:720:25: note: parameter passing for argument of type 'std::initializer_list<gmx::test::{anonymous}::iListInput>' changed in GCC 7.1
720 | std::vector<iListInput> c_InputAnglesZeroAngle = {
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -MF CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o.d -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/listed_forces-test.dir/bonded.cpp.o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target listed_forces-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/haloexchange_mpi.cpp
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF CMakeFiles/domdec-test.dir/hashedmap.cpp.o.d -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_butaneUA_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethaneUA_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_methane_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/range.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethane_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterThreeSite_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFourSite_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFlexAngle_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_twoMoltypes_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroupsCog_ComputesCogs_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:137:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
137 | updateGroupsCog.addCogs(globalAtomIndices, positions);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:137:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target domdec-mpi-test
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringutil.cpp.o -MF CMakeFiles/utility-test.dir/stringutil.cpp.o.d -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/expanded.cpp.o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 70%] Built target mdlib-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/template_mp.cpp.o -MF CMakeFiles/utility-test.dir/template_mp.cpp.o.d -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/template_mp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 71%] Built target domdec-test
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o -MF CMakeFiles/fft-test.dir/fft.cpp.o.d -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 71%] Built target fft-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textwriter.cpp.o -MF CMakeFiles/utility-test.dir/textwriter.cpp.o.d -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static void gmx::test::{anonymous}::PmeGatherTest::SetUpTestCase()':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:80:80: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
80 | 2.86F, 0.24F, 5.76F, 5.19F, 0.72F };
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:119:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
119 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:147:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
147 | };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/typetraits.cpp.o -MF CMakeFiles/utility-test.dir/typetraits.cpp.o.d -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -MF CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o.d -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/listoflists.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/range.cpp.o CMakeFiles/utility-test.dir/strconvert.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/template_mp.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 73%] Built target utility-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; <template-parameter-2-2> = void; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:653:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
653 | vector(_InputIterator __first, _InputIterator __last,
| ^~~~~~
/usr/include/c++/10/bits/stl_vector.h:653:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:340:81: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
340 | c_sampleCoordinatesFull.begin() + 1);
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:343:81: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
343 | c_sampleCoordinatesFull.begin() + 3);
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:346:83: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
346 | c_sampleCoordinatesFull.begin() + 16);
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp: In function 'void gmx::test::pmeInitAtoms(gmx_pme_t*, gmx::StatePropagatorDataGpu*, gmx::test::CodePath, const CoordinatesVector&, const ChargesVector&)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp:202:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
202 | stateGpu->copyCoordinatesToGpu(arrayRefFromArray(coordinates.data(), coordinates.size()),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
203 | gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/clfftinitializer.cpp
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -MF CMakeFiles/hardware-test.dir/cpuinfo.cpp.o.d -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/cpuinfo.cpp
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -MF CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o.d -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/device_availability.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 74%] Built target ewald-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/device_stream_manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/device_management.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -MF CMakeFiles/math-test.dir/coordinatetransformation.cpp.o.d -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/cpuinfo.cpp.o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/hardware-test.dir/device_management.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 74%] Built target hardware-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -MF CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/pinnedmemorychecker.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfit.cpp.o -MF CMakeFiles/math-test.dir/densityfit.cpp.o.d -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 75%] Built target mdrunutility-test-shared
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::AffineTransformationTest_applyTransformationToVectors_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:215:85: note: parameter passing for argument of type 'gmx::Matrix3x3ConstSpan' {aka 'gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >'} changed in GCC 7.1
215 | const AffineTransformation affineTransformation(transformMatrix, transformVector);
| ^
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::AffineTransformationTest_identityTransformYieldsSameVectors_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:199:93: note: parameter passing for argument of type 'gmx::Matrix3x3ConstSpan' {aka 'gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >'} changed in GCC 7.1
199 | const AffineTransformation identityTransformation(identityMatrix<real, 3>(), { 0, 0, 0 });
| ^
/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -MF CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o.d -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/accessor_policy.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_identityTransformation_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:91:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
91 | translateAndScale(toBeTransformed);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_translationWithIdentityScaling_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:98:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
98 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingWithZeroTranslation_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:108:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
108 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_translationAndScalingNonTrivial_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:118:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
118 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingIdentity_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:140:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
140 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingNonTrivial_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:150:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
150 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingInverseNoZero_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:170:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
170 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:171:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
171 | scale.inverseIgnoringZeroScale(testVectors_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingInverseWithOneScaleDimensionZero_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:179:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
179 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:180:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
180 | scale.inverseIgnoringZeroScale(testVectors_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdtypes/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/tests/checkpointdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extents.cpp.o -MF CMakeFiles/mdspan-test.dir/extents.cpp.o.d -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extents.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/dofit.cpp.o -MF CMakeFiles/math-test.dir/dofit.cpp.o.d -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extensions.cpp.o -MF CMakeFiles/mdspan-test.dir/extensions.cpp.o.d -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extensions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -MF CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o.d -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/exponentialmovingaverage.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:58:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:111:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
111 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:111:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const DeviceInformation&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:101:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
101 | void runTest(const DeviceInformation& deviceInfo, ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:101:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:211:16: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
211 | runTest(testDevice->deviceInfo(), makeArrayRef(input), makeArrayRef(output));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:211:16: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:211:16: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:58:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const DeviceInformation&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:101:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
101 | void runTest(const DeviceInformation& deviceInfo, ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:101:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:211:16: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
211 | runTest(testDevice->deviceInfo(), makeArrayRef(input), makeArrayRef(output));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:211:16: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:211:16: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/layouts.cpp.o -MF CMakeFiles/mdspan-test.dir/layouts.cpp.o.d -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/layouts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/device_buffer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -MF CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/typecasts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 75%] Built target gpu_utils-test
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/mdspan.cpp.o -MF CMakeFiles/mdspan-test.dir/mdspan.cpp.o.d -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/mdspan.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/tests/forcebuffers.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/gausstransform.cpp.o -MF CMakeFiles/math-test.dir/gausstransform.cpp.o.d -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 75%] Built target mdtypes-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -MF CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o.d -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 76%] Built target onlinehelp-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 76%] Built target mdspan-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -MF CMakeFiles/random-test.dir/exponentialdistribution.cpp.o.d -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp: In member function 'virtual void gmx::test::{anonymous}::COMInPlaceTest_MatrixDefault_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp:168:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
168 | placeCoordinatesWithCOMInBox(pbcType, unitcell, center, box, testCoordinates_, testTopology_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
169 | COMShiftType::Molecule);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp:182:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
182 | placeCoordinatesWithCOMInBox(pbcType, unitcell, center, box, testCoordinates_, testTopology_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | COMShiftType::Residue);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp: In member function 'virtual void gmx::test::{anonymous}::MatrixTest_transposeWorks_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp:174:70: note: parameter passing for argument of type 'gmx::Matrix3x3ConstSpan' {aka 'gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >'} changed in GCC 7.1
174 | const Matrix3x3 transposedAsymmetricMat = transpose(asymmetricMat);
| ^
/<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp: In member function 'virtual void gmx::test::{anonymous}::MatrixTest_transposeOfSymmetricMatrix_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp:189:68: note: parameter passing for argument of type 'gmx::Matrix3x3ConstSpan' {aka 'gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >'} changed in GCC 7.1
189 | const Matrix3x3 transposedSymmetricMat = transpose(symmetricMat);
| ^
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx::BasicVector<double> > gmx::test::{anonymous}::initialCoordinates()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp: In member function 'virtual void gmx::test::{anonymous}::ShiftTest_CoordinateShiftWorks_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp:195:15: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
195 | shiftAtoms(shift, coords);
| ~~~~~~~~~~^~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/multidimarray.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/random/uniformrealdistribution.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/random/exponentialdistribution.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ExponentialDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/mshift.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/random/uniformrealdistribution.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/random/exponentialdistribution.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/gammadistribution.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::GammaDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/mshift.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/neldermead.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx::BasicVector<double> > gmx::test::{anonymous}::coordinatesWhole()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx::BasicVector<double> > gmx::test::{anonymous}::coordinates()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbc.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/neldermead.cpp: In static member function 'static real gmx::test::{anonymous}::NelderMeadSimplexTest::doubleFirstCoordinateValue(gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/neldermead.cpp:75:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
75 | static real doubleFirstCoordinateValue(ArrayRef<const real> x) { return 2 * x[0]; }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/optimization.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/random/uniformrealdistribution.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/random/normaldistribution.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbcenums.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::NormalDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF CMakeFiles/options-test.dir/repeatingsection.cpp.o.d -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/optimization.cpp: In function 'real gmx::test::{anonymous}::mcCormick(gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/optimization.cpp:61:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | real mcCormick(ArrayRef<const real> x)
| ^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/com.cpp.o CMakeFiles/pbcutil-test.dir/mshift.cpp.o CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 76%] Built target pbcutil-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 76%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_InternalCounterSequence_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Using40Rounds_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Default_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Fast_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:117:54: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
117 | const std::vector<uint64_t> bitsZero{ { 0, 0, 0, 0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:127:87: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
127 | 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:136:86: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
136 | 0xa4093822299f31d0ULL, 0x082efa98ec4e6c89ULL } };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/vectypes.cpp.o -MF CMakeFiles/math-test.dir/vectypes.cpp.o.d -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 77%] Built target options-test
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:46:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/random/uniformrealdistribution.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_GenerateCanonical_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:46:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro 'GMX_TEST_THROW_'
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = const double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'std::enable_if_t<is_same_v<typename std::remove_const<_Tp>::type, typename std::remove_const<U>::type>, void> gmx::test::compareViewsIgnoreConst(gmx::ArrayRef<T>, gmx::ArrayRef<U>) [with T = double; U = const double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
100 | compareViewsIgnoreConst(ArrayRef<T> input, ArrayRef<U> output)
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:111:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
111 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:111:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'std::enable_if_t<is_same_v<typename std::remove_const<_Tp>::type, typename std::remove_const<U>::type>, void> gmx::test::compareViewsIgnoreConst(gmx::ArrayRef<T>, gmx::ArrayRef<U>) [with T = gmx::BasicVector<double>; U = const gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
100 | compareViewsIgnoreConst(ArrayRef<T> input, ArrayRef<U> output)
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = const gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 78%] Built target random-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 79%] Built target table-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 79%] Built target taskassignment-test
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/mtop.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 79%] Built target pull-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/mp11.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/neldermead.cpp.o CMakeFiles/math-test.dir/optimization.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target math-test
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::{anonymous}::Entropy::runQuasiHarmonic(real, gmx_bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::{anonymous}::Entropy::runSchlitter(real, gmx_bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/mp11.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target compat-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/idef.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 82%] Built target topology-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 83%] Built target gmxana-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 84%] Built target pdb2gmx3-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 84%] Built target pdb2gmx2-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_integer.cpp.o -MF CMakeFiles/simd-test.dir/simd_integer.cpp.o.d -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/autocorr.cpp.o -MF CMakeFiles/correlations-test.dir/autocorr.cpp.o.d -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genion.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacCos_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP1_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacNormal_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP4_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP0_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacVector_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacRcross_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP2_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP3_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacNoNormalize_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -MF CMakeFiles/correlations-test.dir/correlationdataset.cpp.o.d -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/correlationdataset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 84%] Built target pdb2gmx1-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/expfit.cpp.o -MF CMakeFiles/correlations-test.dir/expfit.cpp.o.d -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genrestr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp:51:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void gmx::{anonymous}::ExpfitTest::SetUpTestCase()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -MF CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o.d -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_EmptyOnCreate_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_NoNameFromIncorrectTypeNumber_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CannotAddDuplicateEntry_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_AddTypeWorks_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_AddMultipleTypesWorks_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_WrongNameNotFound_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CorrectNameFromTypeNumber_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_IndexOutOfRangeInvalid_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CorrectNameFound_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputPointSet::Value>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputPointSet::Value>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputPointSet::Value>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputPointSet::Value>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValueAndError(int, int, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::test::AnalysisDataTestInputFrame}; _Tp = gmx::test::AnalysisDataTestInputFrame; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputFrame>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputFrame>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'gmx::test::AnalysisDataTestInputFrame& gmx::test::AnalysisDataTestInput::addFrame(real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputFrame*, std::vector<gmx::test::AnalysisDataTestInputFrame> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValueAndError(real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/mock_datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 85%] Built target correlations-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/builder.cpp.o -MF CMakeFiles/coordinateio-test.dir/builder.cpp.o.d -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/builder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 86%] Built target simd-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadapters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o
/usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 86%] Built target analysisdata-test-shared
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target gmxpreprocess-test
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target energyanalysis-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -MF CMakeFiles/coordinateio-test.dir/setatoms.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report_methods.cpp
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/checkpoint.cpp.o -MF CMakeFiles/fileio-test.dir/checkpoint.cpp.o.d -o CMakeFiles/fileio-test.dir/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/checkpoint.cpp
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/trjconv.cpp.o -MF CMakeFiles/tool-test.dir/trjconv.cpp.o.d -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setbothtime.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'testing::Test* testing::internal::ParameterizedTestFactory<TestClass>::CreateTest() [with TestClass = {anonymous}::StructureIORoundtripTest_ReadWriteTpsConf_Test]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/helpwriting.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target tool-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -MF CMakeFiles/coordinateio-test.dir/settimestep.cpp.o.d -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/testmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcserializer.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const {anonymous}::NeighborhoodSearchTestData::RefPair&}; _Tp = {anonymous}::NeighborhoodSearchTestData::RefPair; _Alloc = std::allocator<{anonymous}::NeighborhoodSearchTestData::RefPair>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In function 'void {anonymous}::NeighborhoodSearchTestData::computeReferencesInternal(t_pbc*, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double*&}; _Tp = {anonymous}::NeighborhoodSearchTestData::TestPosition; _Alloc = std::allocator<{anonymous}::NeighborhoodSearchTestData::TestPosition>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void {anonymous}::NeighborhoodSearchTestData::useRefPositionsAsTestPositions()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/poscalc.cpp.o -MF CMakeFiles/selection-test.dir/poscalc.cpp.o.d -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'gmx::AnalysisNeighborhoodPositions {anonymous}::NeighborhoodSearchTestData::testPositions() const':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void {anonymous}::NeighborhoodSearchTest::testPairSearch(gmx::AnalysisNeighborhoodSearch*, const {anonymous}::NeighborhoodSearchTestData&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::BasicVector<double>}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void {anonymous}::NeighborhoodSearchTest::testPairSearchIndexed(gmx::AnalysisNeighborhood*, const {anonymous}::NeighborhoodSearchTestData&, uint64_t)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/include/c++/10/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomTestPositions(int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomTestPositions(int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomRefPositions(int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchExclusions_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSelfPairsSearch_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 88%] Built target coordinateio-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color=
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static const {anonymous}::NeighborhoodSearchTestData& {anonymous}::RandomBoxXYFullPBCData::get()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/densityfittingmodule.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchTriclinic_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearch2DPBC_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSearch_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchBox_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSearchExclusions_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesConcurrentSearches_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSelfPairsSearch_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesNoPBC_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesNullPBC_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesSkippingPairs_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp: In member function 'virtual void gmx::test::{anonymous}::MrcDensityMap_ReadsCoordinateTransformationFromFile_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp:110:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
110 | coordinateTransformation({ &coordinate1, &coordinate1 + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp:111:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
111 | coordinateTransformation({ &coordinate2, &coordinate2 + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformNoOriginGiven_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:89:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
89 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformWithOriginDefined_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:108:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
108 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformWithStartValues_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:126:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
126 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/readinp.cpp.o -MF CMakeFiles/fileio-test.dir/readinp.cpp.o.d -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 88%] Built target mdrun-modules-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/domain_decomposition.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -MF CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/fileioxdrserializer.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/tngio.cpp.o -MF CMakeFiles/fileio-test.dir/tngio.cpp.o.d -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xvgio.cpp.o -MF CMakeFiles/fileio-test.dir/xvgio.cpp.o.d -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pme-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 88%] Built target mdrun-pme-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 89%] Built target selection-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In static member function 'static void gmx::test::XvgioTest::compareValues(gmx::basic_mdspan<const double, gmx::extents<-1, -1> >, gmx::basic_mdspan<const double, gmx::extents<-1, -1> >)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:75:17: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
75 | static void compareValues(basic_mdspan<const double, dynamicExtents2D> ref,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:75:17: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In member function 'virtual void gmx::test::XvgioTest_readXvgIgnoreCommentLineWorks_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:150:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
150 | compareValues(xvgRefData.asConstView(), xvgTestData.asConstView());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:150:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In member function 'virtual void gmx::test::XvgioTest_readXvgRealWorks_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:132:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
132 | compareValues(xvgRefData.asConstView(), xvgTestData.asConstView());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:132:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In member function 'virtual void gmx::test::XvgioTest_readXvgIntWorks_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:113:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
113 | compareValues(xvgRefData.asConstView(), xvgTestData.asConstView());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:113:18: note: parameter passing for argument of type 'gmx::basic_mdspan<const double, gmx::extents<-1, -1> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/checkpoint.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/ewaldsurfaceterm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/checkpoint.cpp.o CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/xvgio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 90%] Built target fileio-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/exactcontinuation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -MF CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o.d -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multiple_time_stepping.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/orires.cpp.o -MF CMakeFiles/mdrun-test.dir/orires.cpp.o.d -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/periodicactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 91%] Built target mdrun-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 92%] Built target mdrun-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 92%] Built target mdrun-mpi-coordination-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 92%] Built target mdrun-simulator-comparison-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/outputfiles.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-io-test.dir/termination.cpp.o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target mdrun-io-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/normalmodes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -MF CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target mdrun-output-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/freeenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target mdrun-mpi-pme-test
/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/box.cpp.o -MF CMakeFiles/nblib-setup-test.dir/box.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/box.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target mdrun-tpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -MF CMakeFiles/nblib-setup-test.dir/interactions.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/particletype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simple_mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/pbcholder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunfep-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrunfep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target mdrunfep-test
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/molecules.cpp
/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 94%] Built target mdrun-non-integrator-test
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp:44:
/<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_GmxForceCalculatorCanCompute_Test::TestBody()':
/<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp:66:48: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
66 | EXPECT_NO_THROW(gmxForceCalculator->compute(simState.coordinates(), simState.forces()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp:66:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp:66:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp
/usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/bondtypes.cpp
/<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_IntegratorWorks_Test::TestBody()':
/<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp:124:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
124 | integrator.integrate(dt, simulationState.coordinates(), simulationState.velocities(),
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
125 | simulationState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp:124:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp:124:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp:124:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so ../../../lib/libgtest.so -lpthread ../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 94%] Built target nblib-integrator-test
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/nbnxnsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/helpers.cpp
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:45:
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_SpcMethanolForcesAreCorrect_Test::TestBody()':
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:82:44: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
82 | ASSERT_NO_THROW(forceCalculator.compute(simState.coordinates(), forces));
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:82:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:82:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_CanIntegrateSystem_Test::TestBody()':
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:119:32: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
119 | forceCalculator.compute(simState.coordinates(), simState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:119:32: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:119:32: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:45:
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:120:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
120 | EXPECT_NO_THROW(integrator.integrate(1.0, simState.coordinates(), simState.velocities(),
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
121 | simState.forces()));
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:120:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:120:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:120:45: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_ArgonForcesAreCorrect_Test::TestBody()':
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:207:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
207 | forceCalculator.compute(simState.coordinates(), simState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:207:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:207:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_ExpectedNumberOfForces_Test::TestBody()':
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:99:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
99 | forceCalculator.compute(simState.coordinates(), forces);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:99:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:99:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_UpdateChangesForces_Test::TestBody()':
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:153:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
153 | forceCalculator.compute(simState.coordinates(), simState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:153:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:153:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:163:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
163 | forceCalculator.compute(simState.coordinates(), forces);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:163:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:163:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:175:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
175 | integrator.integrate(1.0, simState.coordinates(), simState.velocities(), simState.forces());
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:175:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:175:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:175:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:181:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
181 | forceCalculator.compute(simState.coordinates(), forces);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:181:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:181:28: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/util/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/util/tests/setup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/simstate.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/api/nblib/util/tests/setup.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {float, float, float}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_checkNumericValuesHasNan_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_checkNumericValuesHasInf_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/util/tests/traits.cpp
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/kernels.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nblib::StrongType<double, nblib::MassParameter>}; _Tp = nblib::StrongType<double, nblib::MassParameter>; _Alloc = std::allocator<nblib::StrongType<double, nblib::MassParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::StrongType<double, nblib::MassParameter> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so ../../../lib/libgtest.so -lpthread ../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target nblib-integration-test
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::ParticleType&}; _Tp = nblib::ParticleType; _Alloc = std::allocator<nblib::ParticleType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::ParticleType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_TopologyHasParticleTypeIds_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::ParticleType*, std::vector<nblib::ParticleType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-internal.h:58,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:47,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<std::tuple<int, int>&&>, std::tuple<>}; _Key = std::tuple<int, int>; _Val = std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >; _KeyOfValue = std::_Select1st<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >; _Compare = std::less<std::tuple<int, int> >; _Alloc = std::allocator<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >]':
/usr/include/c++/10/bits/stl_tree.h:2460:7: note: parameter passing for argument of type 'std::_Rb_tree<std::tuple<int, int>, std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >, std::_Select1st<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >, std::less<std::tuple<int, int> >, std::allocator<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >::const_iterator' changed in GCC 7.1
2460 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-internal.h:58,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:47,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = std::tuple<int, int>; _Tp = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; _Compare = std::less<std::tuple<int, int> >; _Alloc = std::allocator<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >]':
/usr/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type 'std::_Rb_tree<std::tuple<int, int>, std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >, std::_Select1st<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >, std::less<std::tuple<int, int> >, std::allocator<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >::const_iterator' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_TopologyListedInteractions_Test::TestBody()':
/usr/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type 'std::_Rb_tree<std::tuple<int, int>, std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >, std::_Select1st<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >, std::less<std::tuple<int, int> >, std::allocator<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >::const_iterator' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-util-test.dir/setup.cpp.o CMakeFiles/nblib-util-test.dir/traits.cpp.o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target nblib-util-test
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>}; _Tp = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_TopologyHasMasses_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::StrongType<double, nblib::MassParameter>*, std::vector<nblib::StrongType<double, nblib::MassParameter> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void nblib::test::{anonymous}::NBlibTest_TopologyCanAggregateBonds_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >::<lambda(const auto:24&, const auto:25&)> >]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>]':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/api/nblib/listed_forces/dataflow.hpp:53,
from /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-setup-test.dir/box.cpp.o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o CMakeFiles/nblib-setup-test.dir/topology.cpp.o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so ../../../lib/libgtest.so -lpthread ../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp:56:37: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
56 | std::vector<std::vector<gmx::RVec>> c_coordinatesForTests = {
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp:56:37: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp:56:37: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target nblib-setup-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/conversions.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
In file included from /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp:54:
/<<PKGBUILDDIR>>/api/nblib/listed_forces/dataflow.hpp: In function 'auto nblib::computeForces(const std::vector<T>&, const std::vector<TwoCenterType>&, gmx::ArrayRef<const gmx::BasicVector<double> >, Buffer*, const Pbc&) [with Index = std::array<int, 3>; InteractionType = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; Buffer = std::vector<gmx::BasicVector<double> >; Pbc = nblib::PbcHolder]':
/<<PKGBUILDDIR>>/api/nblib/listed_forces/dataflow.hpp:392:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
392 | auto computeForces(const std::vector<Index>& indices,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/dataflow.hpp: In function 'auto nblib::computeForces(const std::vector<T>&, const std::vector<TwoCenterType>&, gmx::ArrayRef<const gmx::BasicVector<double> >, Buffer*, const Pbc&) [with Index = std::array<int, 4>; InteractionType = nblib::HarmonicAngleType; Buffer = std::vector<gmx::BasicVector<double> >; Pbc = nblib::PbcHolder]':
/<<PKGBUILDDIR>>/api/nblib/listed_forces/dataflow.hpp:392:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/conversions.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/conversions.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void nblib::detail::transferParameters(const InteractionData&, gmx_ffparams_t&) [with InteractionData = nblib::ListedTypeData<nblib::ProperDihedral>]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void nblib::detail::transferParameters(const InteractionData&, gmx_ffparams_t&) [with InteractionData = nblib::ListedTypeData<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void nblib::detail::transferParameters(const InteractionData&, gmx_ffparams_t&) [with InteractionData = nblib::ListedTypeData<nblib::HarmonicAngleType>]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::tuple<std::unique_ptr<InteractionDefinitions, std::default_delete<InteractionDefinitions> >, std::unique_ptr<gmx_ffparams_t, std::default_delete<gmx_ffparams_t> > > nblib::createFFparams(const ListedInteractionData&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /usr/include/c++/10/valarray:38,
from /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp: In member function 'virtual void nblib::test::{anonymous}::LinearChainDataFixture_Multithreading_Test::TestBody()':
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp:234:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
234 | lfCalculator.compute(x, forces, energies);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp:234:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp:234:25: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /usr/include/c++/10/valarray:38,
from /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'nblib::LinearChainData::LinearChainData(int, float)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/transformations.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target mdrunutility-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 97%] Built target nblib-listed-forces-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/filenm.cpp.o -MF CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 97%] Built target mdrunutility-test
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/pargs.cpp.o -MF CMakeFiles/commandline-test.dir/pargs.cpp.o.d -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/average.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target commandline-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF CMakeFiles/analysisdata-test.dir/histogram.cpp.o.d -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp
/usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target nblib-tests
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target analysisdata-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/functional:62,
from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/10/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void {anonymous}::SurfaceAreaTest::generateRandomPositions(int)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesSinglePoint_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPoints_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPointsOfUnequalRadius_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints12_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints32_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints42_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints122_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target trajectoryanalysis-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
(cd build/basic-dp; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic-dp/lib ctest -V || dpkg-architecture -i hurd-i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic-dp
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: NbLibListedForcesTests
1: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/nblib-listed-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/NbLibListedForcesTests.xml"
1: Test timeout computed to be: 600
1: [==========] Running 23 tests from 9 test cases.
1: [----------] Global test environment set-up.
1: [----------] 5 tests from NBlibTest
1: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks
1: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms)
1: [ RUN ] NBlibTest.BondTypesLessThanWorks
1: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms)
1: [ RUN ] NBlibTest.CanSplitListedWork
1: [ OK ] NBlibTest.CanSplitListedWork (0 ms)
1: [ RUN ] NBlibTest.ListedForceBuffer
1: [ OK ] NBlibTest.ListedForceBuffer (0 ms)
1: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct
1: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms)
1: [----------] 5 tests from NBlibTest (1 ms total)
1:
1: [----------] 1 test from Kernels
1: [ RUN ] Kernels.HarmonicScalarKernelCanCompute
1: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms)
1: [----------] 1 test from Kernels (0 ms total)
1:
1: [----------] 5 tests from ListedExampleData
1: [ RUN ] ListedExampleData.ComputeHarmonicBondForces
1: [ OK ] ListedExampleData.ComputeHarmonicBondForces (34 ms)
1: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies
1: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (1 ms)
1: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces
1: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (1 ms)
1: [ RUN ] ListedExampleData.CanReduceForces
1: [ OK ] ListedExampleData.CanReduceForces (47 ms)
1: [ RUN ] ListedExampleData.CanReduceEnergies
1: [ OK ] ListedExampleData.CanReduceEnergies (0 ms)
1: [----------] 5 tests from ListedExampleData (88 ms total)
1:
1: [----------] 1 test from LinearChainDataFixture
1: [ RUN ] LinearChainDataFixture.Multithreading
1: [ OK ] LinearChainDataFixture.Multithreading (1 ms)
1: [----------] 1 test from LinearChainDataFixture (3 ms total)
1:
1: [----------] 1 test from ListedShims
1: [ RUN ] ListedShims.ParameterConversion
1: [ OK ] ListedShims.ParameterConversion (0 ms)
1: [----------] 1 test from ListedShims (2 ms total)
1:
1: [----------] 1 test from ListedTransformations
1: [ RUN ] ListedTransformations.SortInteractionIndices
1: [ OK ] ListedTransformations.SortInteractionIndices (0 ms)
1: [----------] 1 test from ListedTransformations (1 ms total)
1:
1: [----------] 3 tests from FourCenter/ProperDihedralTest
1: [ RUN ] FourCenter/ProperDihedralTest.CheckListed/0
1: [ OK ] FourCenter/ProperDihedralTest.CheckListed/0 (0 ms)
1: [ RUN ] FourCenter/ProperDihedralTest.CheckListed/1
1: [ OK ] FourCenter/ProperDihedralTest.CheckListed/1 (1 ms)
1: [ RUN ] FourCenter/ProperDihedralTest.CheckListed/2
1: [ OK ] FourCenter/ProperDihedralTest.CheckListed/2 (1 ms)
1: [----------] 3 tests from FourCenter/ProperDihedralTest (5 ms total)
1:
1: [----------] 3 tests from TwoCenter/HarmonicBondTest
1: [ RUN ] TwoCenter/HarmonicBondTest.CheckListed/0
1: [ OK ] TwoCenter/HarmonicBondTest.CheckListed/0 (1 ms)
1: [ RUN ] TwoCenter/HarmonicBondTest.CheckListed/1
1: [ OK ] TwoCenter/HarmonicBondTest.CheckListed/1 (0 ms)
1: [ RUN ] TwoCenter/HarmonicBondTest.CheckListed/2
1: [ OK ] TwoCenter/HarmonicBondTest.CheckListed/2 (1 ms)
1: [----------] 3 tests from TwoCenter/HarmonicBondTest (5 ms total)
1:
1: [----------] 3 tests from ThreeCenter/HarmonicAngleTest
1: [ RUN ] ThreeCenter/HarmonicAngleTest.CheckListed/0
1: [ OK ] ThreeCenter/HarmonicAngleTest.CheckListed/0 (1 ms)
1: [ RUN ] ThreeCenter/HarmonicAngleTest.CheckListed/1
1: [ OK ] ThreeCenter/HarmonicAngleTest.CheckListed/1 (0 ms)
1: [ RUN ] ThreeCenter/HarmonicAngleTest.CheckListed/2
1: [ OK ] ThreeCenter/HarmonicAngleTest.CheckListed/2 (1 ms)
1: [----------] 3 tests from ThreeCenter/HarmonicAngleTest (4 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 23 tests from 9 test cases ran. (118 ms total)
1: [ PASSED ] 23 tests.
1/65 Test #1: NbLibListedForcesTests ................ Passed 3.27 sec
test 2
Start 2: NbLibSamplesTestArgon
2: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/argon-forces-integration
2: Test timeout computed to be: 1500
2: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000
2: final forces on particle 0: x -0.412988 y -1.098243 z -0.113189
2: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000
2: final position of particle 0: x 0.789162 y 1.271508 z 0.819867
2/65 Test #2: NbLibSamplesTestArgon ................. Passed 0.14 sec
test 3
Start 3: NbLibSamplesTestMethaneWater
3: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/methane-water-integration
3: Test timeout computed to be: 1500
3: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000
3: final position of particle 9: x 0.151648 y 4.370903 z 5.083184
3/65 Test #3: NbLibSamplesTestMethaneWater .......... Passed 0.13 sec
test 4
Start 4: NbLibUtilTests
4: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/nblib-util-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/NbLibUtilTests.xml"
4: Test timeout computed to be: 30
4: [==========] Running 16 tests from 2 test cases.
4: [----------] Global test environment set-up.
4: [----------] 6 tests from NBlibTest
4: [ RUN ] NBlibTest.isRealValued
4: [ OK ] NBlibTest.isRealValued (0 ms)
4: [ RUN ] NBlibTest.checkNumericValuesHasNan
4: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms)
4: [ RUN ] NBlibTest.checkNumericValuesHasInf
4: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms)
4: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect
4: Velocities were taken from a Maxwell distribution at 300 K
4: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (2 ms)
4: [ RUN ] NBlibTest.generateVelocitySize
4: Velocities were taken from a Maxwell distribution at 300 K
4: [ OK ] NBlibTest.generateVelocitySize (1 ms)
4: [ RUN ] NBlibTest.generateVelocityCheckNumbers
4: Velocities were taken from a Maxwell distribution at 300 K
4: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms)
4: [----------] 6 tests from NBlibTest (4 ms total)
4:
4: [----------] 10 tests from NblibTraitsUtils
4: [ RUN ] NblibTraitsUtils.FuseTwo
4: [ OK ] NblibTraitsUtils.FuseTwo (0 ms)
4: [ RUN ] NblibTraitsUtils.Fuse
4: [ OK ] NblibTraitsUtils.Fuse (0 ms)
4: [ RUN ] NblibTraitsUtils.Repeat
4: [ OK ] NblibTraitsUtils.Repeat (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTuple1
4: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTuple2
4: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTypeList1
4: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTypeList2
4: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms)
4: [ RUN ] NblibTraitsUtils.Contains
4: [ OK ] NblibTraitsUtils.Contains (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated
4: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated
4: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (1 ms)
4: [----------] 10 tests from NblibTraitsUtils (3 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 16 tests from 2 test cases ran. (8 ms total)
4: [ PASSED ] 16 tests.
4/65 Test #4: NbLibUtilTests ........................ Passed 0.08 sec
test 5
Start 5: NbLibSetupTests
5: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/nblib-setup-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/NbLibSetupTests.xml"
5: Test timeout computed to be: 600
5: [==========] Running 39 tests from 1 test case.
5: [----------] Global test environment set-up.
5: [----------] 39 tests from NBlibTest
5: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN
5: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms)
5: [ RUN ] NBlibTest.CubicBoxCannotHaveInf
5: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms)
5: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN
5: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms)
5: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf
5: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms)
5: [ RUN ] NBlibTest.CubicBoxWorks
5: [ OK ] NBlibTest.CubicBoxWorks (0 ms)
5: [ RUN ] NBlibTest.NonBondedForceParamsCorrect
5: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms)
5: [ RUN ] NBlibTest.CanMergeInteractions
5: [ OK ] NBlibTest.CanMergeInteractions (1 ms)
5: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed
5: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms)
5: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed
5: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms)
5: [ RUN ] NBlibTest.PbcHolderWorks
5: [ OK ] NBlibTest.PbcHolderWorks (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms)
5: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule
5: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms)
5: [ RUN ] NBlibTest.CanConstructExclusionListFromNames
5: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms)
5: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed
5: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (1 ms)
5: [ RUN ] NBlibTest.AtWorks
5: [ OK ] NBlibTest.AtWorks (0 ms)
5: [ RUN ] NBlibTest.AtThrows
5: [ OK ] NBlibTest.AtThrows (0 ms)
5: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass
5: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms)
5: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass
5: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (1 ms)
5: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName
5: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms)
5: [ RUN ] NBlibTest.CanAddInteractions
5: [ OK ] NBlibTest.CanAddInteractions (0 ms)
5: [ RUN ] NBlibTest.TopologyHasNumParticles
5: [ OK ] NBlibTest.TopologyHasNumParticles (1 ms)
5: [ RUN ] NBlibTest.TopologyHasCharges
5: [ OK ] NBlibTest.TopologyHasCharges (0 ms)
5: [ RUN ] NBlibTest.TopologyHasMasses
5: [ OK ] NBlibTest.TopologyHasMasses (1 ms)
5: [ RUN ] NBlibTest.TopologyHasParticleTypes
5: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms)
5: [ RUN ] NBlibTest.TopologyHasParticleTypeIds
5: [ OK ] NBlibTest.TopologyHasParticleTypeIds (1 ms)
5: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType
5: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms)
5: [ RUN ] NBlibTest.TopologyHasExclusions
5: [ OK ] NBlibTest.TopologyHasExclusions (1 ms)
5: [ RUN ] NBlibTest.TopologyHasSequencing
5: [ OK ] NBlibTest.TopologyHasSequencing (0 ms)
5: [ RUN ] NBlibTest.TopologyCanAggregateBonds
5: [ OK ] NBlibTest.TopologyCanAggregateBonds (1 ms)
5: [ RUN ] NBlibTest.TopologyCanSequencePairIDs
5: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms)
5: [ RUN ] NBlibTest.TopologySequenceIdThrows
5: No particle O-Atom in residue SOL in molecule SOL found
5: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms)
5: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds
5: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (1 ms)
5: [ RUN ] NBlibTest.TopologyListedInteractions
5: [ OK ] NBlibTest.TopologyListedInteractions (1 ms)
5: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes
5: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms)
5: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows
5: No particle Iron in residue SOL in molecule SOL found
5: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms)
5: [ RUN ] NBlibTest.toGmxExclusionBlockWorks
5: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms)
5: [----------] 39 tests from NBlibTest (12 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 39 tests from 1 test case ran. (13 ms total)
5: [ PASSED ] 39 tests.
5/65 Test #5: NbLibSetupTests ....................... Passed 0.09 sec
test 6
Start 6: NbLibIntegrationTests
6: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/nblib-integration-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/NbLibIntegrationTests.xml"
6: Test timeout computed to be: 600
6: [==========] Running 19 tests from 1 test case.
6: [----------] Global test environment set-up.
6: [----------] 19 tests from NBlibTest
6: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute
6: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (4 ms)
6: [ RUN ] NBlibTest.CanSetupStepWorkload
6: [ OK ] NBlibTest.CanSetupStepWorkload (0 ms)
6: [ RUN ] NBlibTest.GmxForceCalculatorCanSetupInteractionConst
6: [ OK ] NBlibTest.GmxForceCalculatorCanSetupInteractionConst (2 ms)
6: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect
6: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (12 ms)
6: [ RUN ] NBlibTest.ExpectedNumberOfForces
6: [ OK ] NBlibTest.ExpectedNumberOfForces (4 ms)
6: [ RUN ] NBlibTest.CanIntegrateSystem
6: [ OK ] NBlibTest.CanIntegrateSystem (3 ms)
6: [ RUN ] NBlibTest.UpdateChangesForces
6: [ OK ] NBlibTest.UpdateChangesForces (3 ms)
6: [ RUN ] NBlibTest.ArgonForcesAreCorrect
6: [ OK ] NBlibTest.ArgonForcesAreCorrect (2 ms)
6: [ RUN ] NBlibTest.CanConstructNbvSetupUtil
6: [ OK ] NBlibTest.CanConstructNbvSetupUtil (1 ms)
6: [ RUN ] NBlibTest.CanConstructSimulationState
6: [ OK ] NBlibTest.CanConstructSimulationState (0 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN
6: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (1 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF
6: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (1 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN
6: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF
6: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (1 ms)
6: [ RUN ] NBlibTest.SimulationStateCanMove
6: [ OK ] NBlibTest.SimulationStateCanMove (0 ms)
6: [ RUN ] NBlibTest.SimulationStateCanAssign
6: [ OK ] NBlibTest.SimulationStateCanAssign (1 ms)
6: [ RUN ] NBlibTest.SimulationStateHasBox
6: [ OK ] NBlibTest.SimulationStateHasBox (0 ms)
6: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates
6: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms)
6: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities
6: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (1 ms)
6: [----------] 19 tests from NBlibTest (36 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 19 tests from 1 test case ran. (37 ms total)
6: [ PASSED ] 19 tests.
6/65 Test #6: NbLibIntegrationTests ................. Passed 0.11 sec
test 7
Start 7: NbLibIntegratorTests
7: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/nblib-integrator-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/NbLibIntegratorTests.xml"
7: Test timeout computed to be: 600
7: [==========] Running 1 test from 1 test case.
7: [----------] Global test environment set-up.
7: [----------] 1 test from NBlibTest
7: [ RUN ] NBlibTest.IntegratorWorks
7: [ OK ] NBlibTest.IntegratorWorks (2 ms)
7: [----------] 1 test from NBlibTest (2 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 1 test from 1 test case ran. (2 ms total)
7: [ PASSED ] 1 test.
7/65 Test #7: NbLibIntegratorTests .................. Passed 0.07 sec
test 8
Start 8: TestUtilsUnitTests
8: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 59 tests from 5 test cases.
8: [----------] Global test environment set-up.
8: [----------] 10 tests from InteractiveTestHelperTest
8: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
8: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (3 ms)
8: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
8: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (2 ms)
8: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
8: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
8: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
8: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
8: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
8: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
8: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
8: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
8: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (1 ms)
8: [----------] 10 tests from InteractiveTestHelperTest (19 ms total)
8:
8: [----------] 34 tests from ReferenceDataTest
8: [ RUN ] ReferenceDataTest.HandlesSimpleData
8: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
8: [ OK ] ReferenceDataTest.HandlesFloatingPointData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
8: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesStringBlockData
8: [ OK ] ReferenceDataTest.HandlesStringBlockData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesVectorData
8: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesSequenceData
8: [ OK ] ReferenceDataTest.HandlesSequenceData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
8: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesIncorrectData
8: [ OK ] ReferenceDataTest.HandlesIncorrectData (2 ms)
8: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
8: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMissingData
8: [ OK ] ReferenceDataTest.HandlesMissingData (2 ms)
8: [ RUN ] ReferenceDataTest.HandlesUncheckedData
8: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
8: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
8: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesAnys
8: [ OK ] ReferenceDataTest.HandlesAnys (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
8: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
8: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
8: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (2 ms)
8: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue
8: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (2 ms)
8: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType
8: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
8: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
8: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
8: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
8: [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
8: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
8: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (2 ms)
8: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
8: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
8: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
8: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (2 ms)
8: [ RUN ] ReferenceDataTest.HandlesReadingValues
8: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (2 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (3 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms)
8: [----------] 34 tests from ReferenceDataTest (41 ms total)
8:
8: [----------] 7 tests from FloatingPointDifferenceTest
8: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
8: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
8: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
8: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
8: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
8: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
8: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
8: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
8: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total)
8:
8: [----------] 4 tests from FloatingPointToleranceTest
8: [ RUN ] FloatingPointToleranceTest.UlpTolerance
8: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
8: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
8: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
8: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
8: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
8: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
8: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
8: [----------] 4 tests from FloatingPointToleranceTest (0 ms total)
8:
8: [----------] 4 tests from XvgTests
8: [ RUN ] XvgTests.CreateFile
8: [ OK ] XvgTests.CreateFile (2 ms)
8: [ RUN ] XvgTests.CheckMissing
8: [ OK ] XvgTests.CheckMissing (2 ms)
8: [ RUN ] XvgTests.CheckExtra
8: [ OK ] XvgTests.CheckExtra (2 ms)
8: [ RUN ] XvgTests.ReadIncorrect
8: [ OK ] XvgTests.ReadIncorrect (2 ms)
8: [----------] 4 tests from XvgTests (9 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 59 tests from 5 test cases ran. (71 ms total)
8: [ PASSED ] 59 tests.
8/65 Test #8: TestUtilsUnitTests .................... Passed 0.24 sec
test 9
Start 9: TestUtilsMpiUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 1 test from 1 test case.
9: [----------] Global test environment set-up.
9: [----------] 1 test from MpiSelfTest
9: [ RUN ] MpiSelfTest.Runs
9: [ OK ] MpiSelfTest.Runs (1 ms)
9: [----------] 1 test from MpiSelfTest (1 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 1 test from 1 test case ran. (2 ms total)
9: [ PASSED ] 1 test.
9/65 Test #9: TestUtilsMpiUnitTests ................. Passed 0.19 sec
test 10
Start 10: UtilityUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 373 tests from 61 test cases.
10: [----------] Global test environment set-up.
10: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (3 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.Move
10: [ OK ] AllocatorTest/0.Move (0 ms)
10: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/0 (4 ms total)
10:
10: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<double, gmx::PageAlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.Move
10: [ OK ] AllocatorTest/1.Move (0 ms)
10: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/1 (1 ms total)
10:
10: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.Move
10: [ OK ] AllocatorTest/2.Move (0 ms)
10: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/2 (1 ms total)
10:
10: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.Move
10: [ OK ] AllocatorTest/3.Move (0 ms)
10: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/3 (0 ms total)
10:
10: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (2 ms)
10: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/4.Move
10: [ OK ] AllocatorTest/4.Move (0 ms)
10: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/4 (2 ms total)
10:
10: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::PageAlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (2 ms)
10: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/5.Move
10: [ OK ] AllocatorTest/5.Move (0 ms)
10: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/5 (2 ms total)
10:
10: [----------] 1 test from AllocatorUntypedTest
10: [ RUN ] AllocatorUntypedTest.Comparison
10: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
10: [----------] 1 test from AllocatorUntypedTest (0 ms total)
10:
10: [----------] 1 test from EmptyArrayRefTest
10: [ RUN ] EmptyArrayRefTest.IsEmpty
10: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
10: [----------] 1 test from EmptyArrayRefTest (0 ms total)
10:
10: [----------] 1 test from EmptyConstArrayRefTest
10: [ RUN ] EmptyConstArrayRefTest.IsEmpty
10: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
10: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
10: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/0 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
10: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/1 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
10: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/2 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
10: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/3 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
10: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (1 ms)
10: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/4 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
10: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/5 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
10: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/6 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
10: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/7 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
10: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/8 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
10: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/9 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
10: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (1 ms)
10: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/10 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
10: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/11 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
10: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (1 ms)
10: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/12 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
10: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/13 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
10: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/14 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
10: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/15 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
10: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/16 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
10: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/17 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
10: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/18 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
10: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/19 (0 ms total)
10:
10: [----------] 2 tests from CStringUtilityTest
10: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison
10: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms)
10: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength
10: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (1 ms)
10: [----------] 2 tests from CStringUtilityTest (1 ms total)
10:
10: [----------] 2 tests from DefaultInitializationAllocator
10: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization
10: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms)
10: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization
10: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms)
10: [----------] 2 tests from DefaultInitializationAllocator (0 ms total)
10:
10: [----------] 4 tests from EnumerationHelpersTest
10: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks
10: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms)
10: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks
10: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms)
10: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe
10: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms)
10: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks
10: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms)
10: [----------] 4 tests from EnumerationHelpersTest (0 ms total)
10:
10: [----------] 9 tests from FixedCapacityVectorTest
10: [ RUN ] FixedCapacityVectorTest.IsEmpty
10: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms)
10: [ RUN ] FixedCapacityVectorTest.PushWorks
10: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.PopWorks
10: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.ClearWorks
10: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks
10: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.AtThrows
10: [ OK ] FixedCapacityVectorTest.AtThrows (1 ms)
10: [ RUN ] FixedCapacityVectorTest.IteratorWorks
10: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks
10: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks
10: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms)
10: [----------] 9 tests from FixedCapacityVectorTest (1 ms total)
10:
10: [----------] 5 tests from InMemorySerializerTest
10: [ RUN ] InMemorySerializerTest.Roundtrip
10: [ OK ] InMemorySerializerTest.Roundtrip (0 ms)
10: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap
10: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms)
10: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap
10: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms)
10: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap
10: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms)
10: [ RUN ] InMemorySerializerTest.SizeIsCorrect
10: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms)
10: [----------] 5 tests from InMemorySerializerTest (0 ms total)
10:
10: [----------] 4 tests from KeyValueTreeSerializerTest
10: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
10: [ OK ] KeyValueTreeSerializerTest.EmptyTree (36 ms)
10: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
10: [ OK ] KeyValueTreeSerializerTest.SimpleObject (1 ms)
10: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
10: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (1 ms)
10: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
10: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (1 ms)
10: [----------] 4 tests from KeyValueTreeSerializerTest (39 ms total)
10:
10: [----------] 6 tests from TreeValueTransformTest
10: [ RUN ] TreeValueTransformTest.SimpleTransforms
10: [ OK ] TreeValueTransformTest.SimpleTransforms (1 ms)
10: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
10: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms)
10: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
10: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms)
10: [ RUN ] TreeValueTransformTest.ObjectFromString
10: [ OK ] TreeValueTransformTest.ObjectFromString (1 ms)
10: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
10: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (1 ms)
10: [ RUN ] TreeValueTransformTest.ScopedTransformRules
10: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms)
10: [----------] 6 tests from TreeValueTransformTest (4 ms total)
10:
10: [----------] 1 test from TreeValueTransformErrorTest
10: [ RUN ] TreeValueTransformErrorTest.ConversionError
10: [ OK ] TreeValueTransformErrorTest.ConversionError (1 ms)
10: [----------] 1 test from TreeValueTransformErrorTest (1 ms total)
10:
10: [----------] 9 tests from ListOfLists
10: [ RUN ] ListOfLists.EmptyListOfListsWorks
10: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms)
10: [ RUN ] ListOfLists.AppendWorks
10: [ OK ] ListOfLists.AppendWorks (0 ms)
10: [ RUN ] ListOfLists.EmptyListWorks
10: [ OK ] ListOfLists.EmptyListWorks (0 ms)
10: [ RUN ] ListOfLists.AppendAccessWorks
10: [ OK ] ListOfLists.AppendAccessWorks (1 ms)
10: [ RUN ] ListOfLists.ClearWorks
10: [ OK ] ListOfLists.ClearWorks (0 ms)
10: [ RUN ] ListOfLists.OutOfRangeAccessThrows
10: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms)
10: [ RUN ] ListOfLists.FrontAndBackWork
10: [ OK ] ListOfLists.FrontAndBackWork (1 ms)
10: [ RUN ] ListOfLists.ExtractsAndRestores
10: [ OK ] ListOfLists.ExtractsAndRestores (0 ms)
10: [ RUN ] ListOfLists.AppendsListOfListsWithOffset
10: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms)
10: [----------] 9 tests from ListOfLists (2 ms total)
10:
10: [----------] 7 tests from LoggerTest
10: [ RUN ] LoggerTest.EmptyLoggerWorks
10: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
10: [ RUN ] LoggerTest.LogsToStream
10: [ OK ] LoggerTest.LogsToStream (1 ms)
10: [ RUN ] LoggerTest.LogsToFile
10: [ OK ] LoggerTest.LogsToFile (1 ms)
10: [ RUN ] LoggerTest.LevelFilteringWorks
10: [ OK ] LoggerTest.LevelFilteringWorks (1 ms)
10: [ RUN ] LoggerTest.LogsToMultipleStreams
10: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms)
10: [ RUN ] LoggerTest.LogsToMultipleFiles
10: [ OK ] LoggerTest.LogsToMultipleFiles (4 ms)
10: [ RUN ] LoggerTest.LogsToStreamAndFile
10: [ OK ] LoggerTest.LogsToStreamAndFile (1 ms)
10: [----------] 7 tests from LoggerTest (9 ms total)
10:
10: [----------] 4 tests from MDModuleNotificationTest
10: [ RUN ] MDModuleNotificationTest.addConsumer
10: [ OK ] MDModuleNotificationTest.addConsumer (0 ms)
10: [ RUN ] MDModuleNotificationTest.addConsumerWithPointerParameter
10: [ OK ] MDModuleNotificationTest.addConsumerWithPointerParameter (0 ms)
10: [ RUN ] MDModuleNotificationTest.addTwoDifferentConsumers
10: [ OK ] MDModuleNotificationTest.addTwoDifferentConsumers (0 ms)
10: [ RUN ] MDModuleNotificationTest.consumerOfTwoResources
10: [ OK ] MDModuleNotificationTest.consumerOfTwoResources (0 ms)
10: [----------] 4 tests from MDModuleNotificationTest (0 ms total)
10:
10: [----------] 4 tests from MutexBasicTest
10: [ RUN ] MutexBasicTest.CanBeMade
10: [ OK ] MutexBasicTest.CanBeMade (0 ms)
10: [ RUN ] MutexBasicTest.CanBeLocked
10: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
10: [ RUN ] MutexBasicTest.CanBeTryLocked
10: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
10: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
10: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
10: [----------] 4 tests from MutexBasicTest (0 ms total)
10:
10: [----------] 3 tests from MutexTaskTest
10: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
10: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (1 ms)
10: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
10: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms)
10: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
10: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
10: [----------] 3 tests from MutexTaskTest (1 ms total)
10:
10: [----------] 2 tests from PathTest
10: [ RUN ] PathTest.StripSourcePrefixWorks
10: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
10: [ RUN ] PathTest.SearchOperationsWork
10: [ OK ] PathTest.SearchOperationsWork (15 ms)
10: [----------] 2 tests from PathTest (16 ms total)
10:
10: [----------] 2 tests from PhysicalNodeCommunicatorTest
10: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
10: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
10: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
10: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
10: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
10:
10: [----------] 5 tests from Range
10: [ RUN ] Range.EmptyRangeWorks
10: [ OK ] Range.EmptyRangeWorks (0 ms)
10: [ RUN ] Range.NonEmptyRangeWorks
10: [ OK ] Range.NonEmptyRangeWorks (0 ms)
10: [ RUN ] Range.BeginEnd
10: [ OK ] Range.BeginEnd (0 ms)
10: [ RUN ] Range.IsInRangeWorks
10: [ OK ] Range.IsInRangeWorks (0 ms)
10: [ RUN ] Range.IteratorWorks
10: [ OK ] Range.IteratorWorks (0 ms)
10: [----------] 5 tests from Range (0 ms total)
10:
10: [----------] 7 tests from StringConvert
10: [ RUN ] StringConvert.NoResultFromEptyString
10: [ OK ] StringConvert.NoResultFromEptyString (0 ms)
10: [ RUN ] StringConvert.ThreeFloatsSuccessfully
10: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms)
10: [ RUN ] StringConvert.OneIntSucessfully
10: [ OK ] StringConvert.OneIntSucessfully (0 ms)
10: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows
10: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms)
10: [ RUN ] StringConvert.ThrowsWhenWrongSize
10: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms)
10: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows
10: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms)
10: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay
10: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms)
10: [----------] 7 tests from StringConvert (1 ms total)
10:
10: [----------] 9 tests from StringUtilityTest
10: [ RUN ] StringUtilityTest.StartsWith
10: [ OK ] StringUtilityTest.StartsWith (0 ms)
10: [ RUN ] StringUtilityTest.EndsWith
10: [ OK ] StringUtilityTest.EndsWith (0 ms)
10: [ RUN ] StringUtilityTest.StripSuffixIfPresent
10: [ OK ] StringUtilityTest.StripSuffixIfPresent (1 ms)
10: [ RUN ] StringUtilityTest.StripString
10: [ OK ] StringUtilityTest.StripString (0 ms)
10: [ RUN ] StringUtilityTest.SplitString
10: [ OK ] StringUtilityTest.SplitString (0 ms)
10: [ RUN ] StringUtilityTest.SplitDelimitedString
10: [ OK ] StringUtilityTest.SplitDelimitedString (1 ms)
10: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
10: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms)
10: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive
10: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms)
10: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength
10: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms)
10: [----------] 9 tests from StringUtilityTest (3 ms total)
10:
10: [----------] 2 tests from FormatStringTest
10: [ RUN ] FormatStringTest.HandlesBasicFormatting
10: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
10: [ RUN ] FormatStringTest.HandlesLongStrings
10: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
10: [----------] 2 tests from FormatStringTest (0 ms total)
10:
10: [----------] 1 test from StringFormatterTest
10: [ RUN ] StringFormatterTest.HandlesBasicFormatting
10: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
10: [----------] 1 test from StringFormatterTest (0 ms total)
10:
10: [----------] 1 test from formatAndJoinTest
10: [ RUN ] formatAndJoinTest.Works
10: [ OK ] formatAndJoinTest.Works (0 ms)
10: [----------] 1 test from formatAndJoinTest (0 ms total)
10:
10: [----------] 1 test from JoinStringsTest
10: [ RUN ] JoinStringsTest.Works
10: [ OK ] JoinStringsTest.Works (1 ms)
10: [----------] 1 test from JoinStringsTest (1 ms total)
10:
10: [----------] 6 tests from ReplaceAllTest
10: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
10: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesNoMatches
10: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
10: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
10: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
10: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
10: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
10: [----------] 6 tests from ReplaceAllTest (0 ms total)
10:
10: [----------] 10 tests from TextLineWrapperTest
10: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
10: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
10: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
10: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (1 ms)
10: [ RUN ] TextLineWrapperTest.WrapsCorrectly
10: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms)
10: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
10: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (1 ms)
10: [ RUN ] TextLineWrapperTest.HandlesIndent
10: [ OK ] TextLineWrapperTest.HandlesIndent (1 ms)
10: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
10: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
10: [ OK ] TextLineWrapperTest.HandlesHangingIndent (1 ms)
10: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
10: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms)
10: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
10: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (1 ms)
10: [----------] 10 tests from TextLineWrapperTest (5 ms total)
10:
10: [----------] 1 test from TemplateMPTest
10: [ RUN ] TemplateMPTest.DispatchTemplatedFunction
10: [ OK ] TemplateMPTest.DispatchTemplatedFunction (0 ms)
10: [----------] 1 test from TemplateMPTest (0 ms total)
10:
10: [----------] 6 tests from TextWriterTest
10: [ RUN ] TextWriterTest.WritesLines
10: [ OK ] TextWriterTest.WritesLines (0 ms)
10: [ RUN ] TextWriterTest.WritesLinesInParts
10: [ OK ] TextWriterTest.WritesLinesInParts (0 ms)
10: [ RUN ] TextWriterTest.WritesWrappedLines
10: [ OK ] TextWriterTest.WritesWrappedLines (0 ms)
10: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
10: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (1 ms)
10: [ RUN ] TextWriterTest.TracksNewlines
10: [ OK ] TextWriterTest.TracksNewlines (0 ms)
10: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
10: [ OK ] TextWriterTest.PreservesTrailingWhitespace (1 ms)
10: [----------] 6 tests from TextWriterTest (3 ms total)
10:
10: [----------] 1 test from TypeTraitsTest
10: [ RUN ] TypeTraitsTest.IsIntegralConstant
10: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
10: [----------] 1 test from TypeTraitsTest (0 ms total)
10:
10: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
10: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total)
10:
10: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
10: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (1 ms total)
10:
10: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
10: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (1 ms total)
10:
10: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (1 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
10: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (2 ms total)
10:
10: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms)
10: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (2 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 373 tests from 61 test cases ran. (114 ms total)
10: [ PASSED ] 373 tests.
10/65 Test #10: UtilityUnitTests ...................... Passed 0.24 sec
test 11
Start 11: UtilityMpiUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 2 tests from 1 test case.
11: [----------] Global test environment set-up.
11: [----------] 2 tests from PhysicalNodeCommunicatorTest
11: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
11: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (5 ms)
11: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
11: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (17 ms)
11: [----------] 2 tests from PhysicalNodeCommunicatorTest (22 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 2 tests from 1 test case ran. (22 ms total)
11: [ PASSED ] 2 tests.
11/65 Test #11: UtilityMpiUnitTests ................... Passed 0.15 sec
test 12
Start 12: MdlibUnitTest
12: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml"
12: Test timeout computed to be: 30
12: [==========] Running 141 tests from 15 test cases.
12: [----------] Global test environment set-up.
12: [----------] 1 test from VerletBufferConstraintTest
12: [ RUN ] VerletBufferConstraintTest.EqualMasses
12: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms)
12: [----------] 1 test from VerletBufferConstraintTest (0 ms total)
12:
12: [----------] 2 tests from PrEbinTest
12: [ RUN ] PrEbinTest.HandlesAverages
12: [ OK ] PrEbinTest.HandlesAverages (25 ms)
12: [ RUN ] PrEbinTest.HandlesEmptyAverages
12: [ OK ] PrEbinTest.HandlesEmptyAverages (2 ms)
12: [----------] 2 tests from PrEbinTest (27 ms total)
12:
12: [----------] 3 tests from EnergyDriftTracker
12: [ RUN ] EnergyDriftTracker.emptyWorks
12: [ OK ] EnergyDriftTracker.emptyWorks (0 ms)
12: [ RUN ] EnergyDriftTracker.onePointWorks
12: [ OK ] EnergyDriftTracker.onePointWorks (0 ms)
12: [ RUN ] EnergyDriftTracker.manyPointsWorks
12: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms)
12: [----------] 3 tests from EnergyDriftTracker (0 ms total)
12:
12: [----------] 4 tests from ShakeTest
12: [ RUN ] ShakeTest.ConstrainsOneBond
12: [ OK ] ShakeTest.ConstrainsOneBond (0 ms)
12: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
12: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
12: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
12: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (1 ms)
12: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
12: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
12: [----------] 4 tests from ShakeTest (1 ms total)
12:
12: [----------] 1 test from NullSignalTest
12: [ RUN ] NullSignalTest.NullSignallerWorks
12: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
12: [----------] 1 test from NullSignalTest (0 ms total)
12:
12: [----------] 7 tests from SignalTest
12: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
12: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
12: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
12: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
12: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
12: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
12: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
12: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
12: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
12: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
12: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
12: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
12: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
12: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
12: [----------] 7 tests from SignalTest (0 ms total)
12:
12: [----------] 9 tests from UpdateGroups
12: [ RUN ] UpdateGroups.ethaneUA
12: [ OK ] UpdateGroups.ethaneUA (1 ms)
12: [ RUN ] UpdateGroups.methane
12: [ OK ] UpdateGroups.methane (0 ms)
12: [ RUN ] UpdateGroups.ethane
12: [ OK ] UpdateGroups.ethane (0 ms)
12: [ RUN ] UpdateGroups.butaneUA
12: [ OK ] UpdateGroups.butaneUA (0 ms)
12: [ RUN ] UpdateGroups.waterThreeSite
12: [ OK ] UpdateGroups.waterThreeSite (0 ms)
12: [ RUN ] UpdateGroups.waterFourSite
12: [ OK ] UpdateGroups.waterFourSite (1 ms)
12: [ RUN ] UpdateGroups.fourAtomsWithSettle
12: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
12: [ RUN ] UpdateGroups.waterFlexAngle
12: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
12: [ RUN ] UpdateGroups.twoMoltypes
12: [ OK ] UpdateGroups.twoMoltypes (0 ms)
12: [----------] 9 tests from UpdateGroups (2 ms total)
12:
12: [----------] 1 test from UpdateGroupsCog
12: [ RUN ] UpdateGroupsCog.ComputesCogs
12: [ OK ] UpdateGroupsCog.ComputesCogs (31 ms)
12: [----------] 1 test from UpdateGroupsCog (31 ms total)
12:
12: [----------] 12 tests from WithParameters/ConstraintsTest
12: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0
12: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1
12: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0
12: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1
12: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms)
12: [----------] 12 tests from WithParameters/ConstraintsTest (5 ms total)
12:
12: [----------] 11 tests from WithParameters/EnergyOutputTest
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (43 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (9 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (12 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3
12: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (4 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file
12:
Reading energy frame 0 time 10.100
Reading energy frame 1 time 27.500
Reading energy frame 2 time 44.900
Reading energy frame 3 time 62.300
Reading energy frame 4 time 79.700
Reading energy frame 5 time 97.100
Reading energy frame 6 time 114.500
Reading energy frame 7 time 131.900
Reading energy frame 8 time 149.300
Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (51 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (14 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (14 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (23 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (14 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (13 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (14 ms)
12: [----------] 11 tests from WithParameters/EnergyOutputTest (234 ms total)
12:
12: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (1 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms)
12: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (2 ms total)
12:
12: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms)
12: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (1 ms total)
12:
12: [----------] 23 tests from WithParameters/FreeEnergyParameterTest
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (1 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (1 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (1 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (1 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms)
12: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (4 ms total)
12:
12: [----------] 16 tests from WithParameters/LeapFrogTest
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (2 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (2 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (12 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (33 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (2 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (12 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (12 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (11 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (12 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (24 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (12 ms)
12: [----------] 16 tests from WithParameters/LeapFrogTest (162 ms total)
12:
12: [----------] 13 tests from WithParameters/SettleTest
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (2 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (2 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (3 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (3 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (6 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (3 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (8 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (5 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (4 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (8 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (8 ms)
12: [----------] 13 tests from WithParameters/SettleTest (62 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 141 tests from 15 test cases ran. (532 ms total)
12: [ PASSED ] 141 tests.
12/65 Test #12: MdlibUnitTest ......................... Passed 1.29 sec
test 13
Start 13: AwhTest
13: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AwhTest.xml"
13: Test timeout computed to be: 30
13: [==========] Running 17 tests from 6 test cases.
13: [----------] Global test environment set-up.
13: [----------] 1 test from BiasTest
13: [ RUN ] BiasTest.DetectsCovering
13: [ OK ] BiasTest.DetectsCovering (4 ms)
13: [----------] 1 test from BiasTest (4 ms total)
13:
13: [----------] 1 test from biasGridTest
13: [ RUN ] biasGridTest.neighborhood
13: [ OK ] biasGridTest.neighborhood (8 ms)
13: [----------] 1 test from biasGridTest (8 ms total)
13:
13: [----------] 1 test from BiasFepLambdaStateTest
13: [ RUN ] BiasFepLambdaStateTest.DetectsCovering
13: [ OK ] BiasFepLambdaStateTest.DetectsCovering (18 ms)
13: [----------] 1 test from BiasFepLambdaStateTest (18 ms total)
13:
13: [----------] 8 tests from WithParameters/BiasTest
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (37 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (10 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (2 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (3 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (3 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (5 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (2 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (3 ms)
13: [----------] 8 tests from WithParameters/BiasTest (70 ms total)
13:
13: [----------] 2 tests from WithParameters/BiasStateTest
13: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
13: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (1 ms)
13: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
13: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (15 ms)
13: [----------] 2 tests from WithParameters/BiasStateTest (18 ms total)
13:
13: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (39 ms)
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (41 ms)
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (38 ms)
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (39 ms)
13: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (169 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 17 tests from 6 test cases ran. (291 ms total)
13: [ PASSED ] 17 tests.
13/65 Test #13: AwhTest ............................... Passed 0.51 sec
test 14
Start 14: DensityFittingAppliedForcesUnitTest
14: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/density_fitting_applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml"
14: Test timeout computed to be: 30
14: [==========] Running 18 tests from 4 test cases.
14: [----------] Global test environment set-up.
14: [----------] 2 tests from DensityFittingTest
14: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows
14: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (4 ms)
14: [ RUN ] DensityFittingTest.SingleAtom
14: [ OK ] DensityFittingTest.SingleAtom (42 ms)
14: [----------] 2 tests from DensityFittingTest (46 ms total)
14:
14: [----------] 7 tests from DensityFittingAmplitudeLookupTest
14: [ RUN ] DensityFittingAmplitudeLookupTest.Unity
14: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.Charge
14: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.Masses
14: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign
14: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (2 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct
14: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign
14: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct
14: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (1 ms)
14: [----------] 7 tests from DensityFittingAmplitudeLookupTest (4 ms total)
14:
14: [----------] 1 test from DensityFittingForceProviderState
14: [ RUN ] DensityFittingForceProviderState.RoundTripSaving
14: [ OK ] DensityFittingForceProviderState.RoundTripSaving (2 ms)
14: [----------] 1 test from DensityFittingForceProviderState (2 ms total)
14:
14: [----------] 8 tests from DensityFittingOptionsTest
14: [ RUN ] DensityFittingOptionsTest.DefaultParameters
14: [ OK ] DensityFittingOptionsTest.DefaultParameters (1 ms)
14: [ RUN ] DensityFittingOptionsTest.OptionSetsActive
14: [ OK ] DensityFittingOptionsTest.OptionSetsActive (1 ms)
14: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive
14: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (1 ms)
14: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive
14: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (2 ms)
14: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup
14: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (2 ms)
14: [ RUN ] DensityFittingOptionsTest.InternalsToKvt
14: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms)
14: [ RUN ] DensityFittingOptionsTest.KvtToInternal
14: [ OK ] DensityFittingOptionsTest.KvtToInternal (2 ms)
14: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent
14: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (1 ms)
14: [----------] 8 tests from DensityFittingOptionsTest (10 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 18 tests from 4 test cases ran. (63 ms total)
14: [ PASSED ] 18 tests.
14/65 Test #14: DensityFittingAppliedForcesUnitTest ... Passed 0.21 sec
test 15
Start 15: AppliedForcesUnitTest
15: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml"
15: Test timeout computed to be: 30
15: [==========] Running 3 tests from 1 test case.
15: [----------] Global test environment set-up.
15: [----------] 3 tests from ElectricFieldTest
15: [ RUN ] ElectricFieldTest.Static
15: [ OK ] ElectricFieldTest.Static (1 ms)
15: [ RUN ] ElectricFieldTest.Oscillating
15: [ OK ] ElectricFieldTest.Oscillating (0 ms)
15: [ RUN ] ElectricFieldTest.Pulsed
15: [ OK ] ElectricFieldTest.Pulsed (0 ms)
15: [----------] 3 tests from ElectricFieldTest (3 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 3 tests from 1 test case ran. (6 ms total)
15: [ PASSED ] 3 tests.
15/65 Test #15: AppliedForcesUnitTest ................. Passed 0.12 sec
test 16
Start 16: ListedForcesTest
16: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/listed_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/ListedForcesTest.xml"
16: Test timeout computed to be: 30
16: [==========] Running 111 tests from 7 test cases.
16: [----------] Global test environment set-up.
16: [----------] 24 tests from Bond/ListedForcesTest
16: [ RUN ] Bond/ListedForcesTest.Ifunc/0
16: [ OK ] Bond/ListedForcesTest.Ifunc/0 (29 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/1
16: [ OK ] Bond/ListedForcesTest.Ifunc/1 (2 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/2
16: [ OK ] Bond/ListedForcesTest.Ifunc/2 (2 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/3
16: [ OK ] Bond/ListedForcesTest.Ifunc/3 (32 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/4
16: [ OK ] Bond/ListedForcesTest.Ifunc/4 (12 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/5
16: [ OK ] Bond/ListedForcesTest.Ifunc/5 (3 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/6
16: [ OK ] Bond/ListedForcesTest.Ifunc/6 (2 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/7
16: [ OK ] Bond/ListedForcesTest.Ifunc/7 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/8
16: [ OK ] Bond/ListedForcesTest.Ifunc/8 (3 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/9
16: [ OK ] Bond/ListedForcesTest.Ifunc/9 (3 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/10
16: [ OK ] Bond/ListedForcesTest.Ifunc/10 (3 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/11
16: [ OK ] Bond/ListedForcesTest.Ifunc/11 (3 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/12
16: [ OK ] Bond/ListedForcesTest.Ifunc/12 (23 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/13
16: [ OK ] Bond/ListedForcesTest.Ifunc/13 (3 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/14
16: [ OK ] Bond/ListedForcesTest.Ifunc/14 (2 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/15
16: [ OK ] Bond/ListedForcesTest.Ifunc/15 (3 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/16
16: [ OK ] Bond/ListedForcesTest.Ifunc/16 (3 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/17
16: [ OK ] Bond/ListedForcesTest.Ifunc/17 (3 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/18
16: [ OK ] Bond/ListedForcesTest.Ifunc/18 (2 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/19
16: [ OK ] Bond/ListedForcesTest.Ifunc/19 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/20
16: [ OK ] Bond/ListedForcesTest.Ifunc/20 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/21
16: [ OK ] Bond/ListedForcesTest.Ifunc/21 (2 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/22
16: [ OK ] Bond/ListedForcesTest.Ifunc/22 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/23
16: [ OK ] Bond/ListedForcesTest.Ifunc/23 (3 ms)
16: [----------] 24 tests from Bond/ListedForcesTest (147 ms total)
16:
16: [----------] 33 tests from Angle/ListedForcesTest
16: [ RUN ] Angle/ListedForcesTest.Ifunc/0
16: [ OK ] Angle/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/1
16: [ OK ] Angle/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/2
16: [ OK ] Angle/ListedForcesTest.Ifunc/2 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/3
16: [ OK ] Angle/ListedForcesTest.Ifunc/3 (15 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/4
16: [ OK ] Angle/ListedForcesTest.Ifunc/4 (3 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/5
16: [ OK ] Angle/ListedForcesTest.Ifunc/5 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/6
16: [ OK ] Angle/ListedForcesTest.Ifunc/6 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/7
16: [ OK ] Angle/ListedForcesTest.Ifunc/7 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/8
16: [ OK ] Angle/ListedForcesTest.Ifunc/8 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/9
16: [ OK ] Angle/ListedForcesTest.Ifunc/9 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/10
16: [ OK ] Angle/ListedForcesTest.Ifunc/10 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/11
16: [ OK ] Angle/ListedForcesTest.Ifunc/11 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/12
16: [ OK ] Angle/ListedForcesTest.Ifunc/12 (18 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/13
16: [ OK ] Angle/ListedForcesTest.Ifunc/13 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/14
16: [ OK ] Angle/ListedForcesTest.Ifunc/14 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/15
16: [ OK ] Angle/ListedForcesTest.Ifunc/15 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/16
16: [ OK ] Angle/ListedForcesTest.Ifunc/16 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/17
16: [ OK ] Angle/ListedForcesTest.Ifunc/17 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/18
16: [ OK ] Angle/ListedForcesTest.Ifunc/18 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/19
16: [ OK ] Angle/ListedForcesTest.Ifunc/19 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/20
16: [ OK ] Angle/ListedForcesTest.Ifunc/20 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/21
16: [ OK ] Angle/ListedForcesTest.Ifunc/21 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/22
16: [ OK ] Angle/ListedForcesTest.Ifunc/22 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/23
16: [ OK ] Angle/ListedForcesTest.Ifunc/23 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/24
16: [ OK ] Angle/ListedForcesTest.Ifunc/24 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/25
16: [ OK ] Angle/ListedForcesTest.Ifunc/25 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/26
16: [ OK ] Angle/ListedForcesTest.Ifunc/26 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/27
16: [ OK ] Angle/ListedForcesTest.Ifunc/27 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/28
16: [ OK ] Angle/ListedForcesTest.Ifunc/28 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/29
16: [ OK ] Angle/ListedForcesTest.Ifunc/29 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/30
16: [ OK ] Angle/ListedForcesTest.Ifunc/30 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/31
16: [ OK ] Angle/ListedForcesTest.Ifunc/31 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/32
16: [ OK ] Angle/ListedForcesTest.Ifunc/32 (1 ms)
16: [----------] 33 tests from Angle/ListedForcesTest (80 ms total)
16:
16: [----------] 18 tests from Dihedral/ListedForcesTest
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (2 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (2 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (2 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (2 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (2 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (2 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (2 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (2 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (2 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (1 ms)
16: [----------] 18 tests from Dihedral/ListedForcesTest (30 ms total)
16:
16: [----------] 12 tests from Polarize/ListedForcesTest
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/0
16: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/1
16: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/2
16: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/3
16: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/4
16: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/5
16: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/6
16: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/7
16: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/8
16: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/9
16: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/10
16: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/11
16: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (1 ms)
16: [----------] 12 tests from Polarize/ListedForcesTest (12 ms total)
16:
16: [----------] 18 tests from Restraints/ListedForcesTest
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/0
16: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (2 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/1
16: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (2 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/2
16: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (2 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/3
16: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/4
16: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/5
16: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/6
16: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (2 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/7
16: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (2 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/8
16: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (2 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/9
16: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/10
16: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/11
16: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/12
16: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/13
16: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/14
16: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/15
16: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (2 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/16
16: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (2 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/17
16: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (2 ms)
16: [----------] 18 tests from Restraints/ListedForcesTest (30 ms total)
16:
16: [----------] 3 tests from BondZeroLength/ListedForcesTest
16: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0
16: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1
16: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2
16: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms)
16: [----------] 3 tests from BondZeroLength/ListedForcesTest (2 ms total)
16:
16: [----------] 3 tests from AngleZero/ListedForcesTest
16: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0
16: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms)
16: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1
16: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms)
16: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2
16: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms)
16: [----------] 3 tests from AngleZero/ListedForcesTest (3 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 111 tests from 7 test cases ran. (305 ms total)
16: [ PASSED ] 111 tests.
16/65 Test #16: ListedForcesTest ...................... Passed 0.45 sec
test 17
Start 17: CommandLineUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 59 tests from 7 test cases.
17: [----------] Global test environment set-up.
17: [----------] 3 tests from CommandLineHelpModuleTest
17: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
17: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (5 ms)
17: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
17: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (2 ms)
17: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
17: [ OK ] CommandLineHelpModuleTest.ExportsHelp (16 ms)
17: [----------] 3 tests from CommandLineHelpModuleTest (23 ms total)
17:
17: [----------] 7 tests from CommandLineHelpWriterTest
17: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
17: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (5 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
17: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (13 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
17: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (3 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
17: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
17: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (2 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
17: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues
17: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (2 ms)
17: [----------] 7 tests from CommandLineHelpWriterTest (27 ms total)
17:
17: [----------] 6 tests from CommandLineModuleManagerTest
17: [ RUN ] CommandLineModuleManagerTest.RunsModule
17: [ OK ] CommandLineModuleManagerTest.RunsModule (2 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (1 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (1 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (2 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (1 ms)
17: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
17: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (1 ms)
17: [----------] 6 tests from CommandLineModuleManagerTest (8 ms total)
17:
17: [----------] 13 tests from CommandLineParserTest
17: [ RUN ] CommandLineParserTest.HandlesSingleValues
17: [ OK ] CommandLineParserTest.HandlesSingleValues (2 ms)
17: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
17: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
17: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (1 ms)
17: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
17: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (1 ms)
17: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
17: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesString
17: [ OK ] CommandLineParserTest.HandlesString (0 ms)
17: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
17: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (1 ms)
17: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
17: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
17: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (1 ms)
17: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
17: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
17: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
17: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms)
17: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
17: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
17: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
17: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (1 ms)
17: [----------] 13 tests from CommandLineParserTest (10 ms total)
17:
17: [----------] 6 tests from CommandLineProgramContextTest
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
17: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (1 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
17: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (1 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (1 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms)
17: [----------] 6 tests from CommandLineProgramContextTest (4 ms total)
17:
17: [----------] 3 tests from OutputNamesTest
17: [ RUN ] OutputNamesTest.CanBeSuffixed
17: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms)
17: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend
17: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms)
17: [ RUN ] OutputNamesTest.CanHavePartNumberAdded
17: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms)
17: [----------] 3 tests from OutputNamesTest (0 ms total)
17:
17: [----------] 21 tests from ParseCommonArgsTest
17: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
17: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (1 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
17: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
17: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
17: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
17: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
17: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
17: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
17: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
17: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
17: [ OK ] ParseCommonArgsTest.ParsesFileArgs (2 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
17: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (1 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
17: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
17: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
17: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
17: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms)
17: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
17: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (1 ms)
17: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
17: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (1 ms)
17: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
17: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (2 ms)
17: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
17: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms)
17: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
17: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (5 ms)
17: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
17: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (3 ms)
17: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
17: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms)
17: [----------] 21 tests from ParseCommonArgsTest (19 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 59 tests from 7 test cases ran. (93 ms total)
17: [ PASSED ] 59 tests.
17/65 Test #17: CommandLineUnitTests .................. Passed 0.17 sec
test 18
Start 18: DomDecTests
18: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/DomDecTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 9 tests from 2 test cases.
18: [----------] Global test environment set-up.
18: [----------] 7 tests from HashedMap
18: [ RUN ] HashedMap.InsertsFinds
18: [ OK ] HashedMap.InsertsFinds (0 ms)
18: [ RUN ] HashedMap.NegativeKeysWork
18: [ OK ] HashedMap.NegativeKeysWork (0 ms)
18: [ RUN ] HashedMap.InsertsErases
18: [ OK ] HashedMap.InsertsErases (0 ms)
18: [ RUN ] HashedMap.InsertsOrAssigns
18: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
18: [ RUN ] HashedMap.Clears
18: [ OK ] HashedMap.Clears (0 ms)
18: [ RUN ] HashedMap.LinkedEntries
18: [ OK ] HashedMap.LinkedEntries (0 ms)
18: [ RUN ] HashedMap.ResizesTable
18: [ OK ] HashedMap.ResizesTable (0 ms)
18: [----------] 7 tests from HashedMap (0 ms total)
18:
18: [----------] 2 tests from LocalAtomSetManager
18: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
18: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms)
18: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
18: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (1 ms)
18: [----------] 2 tests from LocalAtomSetManager (1 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 9 tests from 2 test cases ran. (2 ms total)
18: [ PASSED ] 9 tests.
18/65 Test #18: DomDecTests ........................... Passed 0.12 sec
test 19
Start 19: DomDecMpiTests
19: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/DomDecMpiTests.xml"
19: Test timeout computed to be: 30
19: [==========] Running 4 tests from 1 test case.
19: [----------] Global test environment set-up.
19: [----------] 4 tests from HaloExchangeTest
19: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse
19: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (3 ms)
19: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses
19: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (4 ms)
19: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim
19: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (4 ms)
19: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1
19: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (3 ms)
19: [----------] 4 tests from HaloExchangeTest (14 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 4 tests from 1 test case ran. (15 ms total)
19: [ PASSED ] 4 tests.
19/65 Test #19: DomDecMpiTests ........................ Passed 0.17 sec
test 20
Start 20: EwaldUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml"
20: Test timeout computed to be: 30
20: [==========] Running 185 tests from 10 test cases.
20: [----------] Global test environment set-up.
20: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (1 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (14 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (1 ms)
20: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (17 ms total)
20:
20: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (68 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (41 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (51 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (14 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (15 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (21 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (27 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (14 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (15 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (14 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (16 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (16 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (55 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (15 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (15 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (34 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (16 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (16 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (16 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (16 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (16 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (17 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (17 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (17 ms)
20: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (585 ms total)
20:
20: [----------] 72 tests from SaneInput/PmeGatherTest
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (20 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (3 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (12 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (3 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (3 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (3 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (3 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (3 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (3 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (9 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (3 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (2 ms)
20: [----------] 72 tests from SaneInput/PmeGatherTest (188 ms total)
20:
20: [----------] 16 tests from SaneInput/PmeSolveTest
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (8 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (10 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (5 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (10 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (9 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (6 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (6 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (5 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (12 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (6 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (11 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (7 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (6 ms)
20: [----------] 16 tests from SaneInput/PmeSolveTest (117 ms total)
20:
20: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (6 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (6 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (4 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (3 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (5 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (6 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (4 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (4 ms)
20: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (39 ms total)
20:
20: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (10 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (10 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (7 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (6 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (10 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (10 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (6 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (6 ms)
20: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (67 ms total)
20:
20: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (6 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (11 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (6 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (11 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (4 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (6 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (4 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (6 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (6 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (11 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (6 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (10 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (6 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (4 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (6 ms)
20: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (108 ms total)
20:
20: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (14 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (11 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (7 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (7 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (9 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (10 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (6 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (7 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (7 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (9 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (11 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (10 ms)
20: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (114 ms total)
20:
20: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (7 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (7 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (8 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (10 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (11 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (13 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (17 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (8 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (9 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (11 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (14 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (15 ms)
20: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (137 ms total)
20:
20: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (17 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (19 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (27 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (30 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (38 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (42 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (18 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (19 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (25 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (28 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (35 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (39 ms)
20: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (363 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 185 tests from 10 test cases ran. (1736 ms total)
20: [ PASSED ] 185 tests.
20/65 Test #20: EwaldUnitTests ........................ Passed 1.95 sec
test 21
Start 21: FFTUnitTests
21: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/FFTUnitTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 14 tests from 4 test cases.
21: [----------] Global test environment set-up.
21: [----------] 2 tests from ManyFFTTest
21: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
21: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (71 ms)
21: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
21: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (44 ms)
21: [----------] 2 tests from ManyFFTTest (119 ms total)
21:
21: [----------] 1 test from FFTTest
21: [ RUN ] FFTTest.Real2DLength18_15Test
21: [ OK ] FFTTest.Real2DLength18_15Test (15 ms)
21: [----------] 1 test from FFTTest (16 ms total)
21:
21: [----------] 1 test from FFFTest3D
21: [ RUN ] FFFTest3D.Real5_6_9
21: [ OK ] FFFTest3D.Real5_6_9 (12 ms)
21: [----------] 1 test from FFFTest3D (14 ms total)
21:
21: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (4 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (9 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (5 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (8 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (7 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (4 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (3 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (2 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (23 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (39 ms)
21: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (110 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 14 tests from 4 test cases ran. (259 ms total)
21: [ PASSED ] 14 tests.
21/65 Test #21: FFTUnitTests .......................... Passed 0.33 sec
test 22
Start 22: GpuUtilsUnitTests
22: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 64 tests from 22 test cases.
22: [----------] Global test environment set-up.
22: [----------] 2 tests from ClfftInitializer
22: [ RUN ] ClfftInitializer.SingleInitializationWorks
22: [ OK ] ClfftInitializer.SingleInitializationWorks (1 ms)
22: [ RUN ] ClfftInitializer.TwoInitializationsWork
22: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms)
22: [----------] 2 tests from ClfftInitializer (1 ms total)
22:
22: [----------] 1 test from DevicesAvailable
22: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice
22: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms)
22: [----------] 1 test from DevicesAvailable (0 ms total)
22:
22: [----------] 1 test from DeviceStreamManagerTest
22: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice
22: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms)
22: [----------] 1 test from DeviceStreamManagerTest (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
22: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/0 (1 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double
22: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/1 (1 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<double>
22: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
22: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/3 (0 ms total)
22:
22: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
22: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
22: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
22: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
22: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
22: [----------] 3 tests from HostAllocatorTestCopyable/0 (1 ms total)
22:
22: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double
22: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
22: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
22: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
22: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
22: [----------] 3 tests from HostAllocatorTestCopyable/1 (1 ms total)
22:
22: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<double>
22: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
22: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
22: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
22: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
22: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
22: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
22: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.Swap
22: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.Comparison
22: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/0 (1 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double
22: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
22: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.Swap
22: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.Comparison
22: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/1 (1 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<double>
22: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
22: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.Swap
22: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.Comparison
22: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/2 (1 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
22: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
22: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.Swap
22: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.Comparison
22: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
22: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
22: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
22: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double
22: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
22: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
22: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<double>
22: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
22: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
22: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total)
22:
22: [----------] 1 test from HostAllocatorUntypedTest
22: [ RUN ] HostAllocatorUntypedTest.Comparison
22: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
22: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
22:
22: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
22: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/0.Move
22: [ OK ] AllocatorTest/0.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/0 (1 ms total)
22:
22: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/1.Move
22: [ OK ] AllocatorTest/1.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/1 (0 ms total)
22:
22: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (2 ms)
22: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/2.Move
22: [ OK ] AllocatorTest/2.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/2 (2 ms total)
22:
22: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (1 ms)
22: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/3.Move
22: [ OK ] AllocatorTest/3.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/3 (1 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 64 tests from 22 test cases ran. (18 ms total)
22: [ PASSED ] 64 tests.
22/65 Test #22: GpuUtilsUnitTests ..................... Passed 0.29 sec
test 23
Start 23: HardwareUnitTests
23: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 6 tests from 3 test cases.
23: [----------] Global test environment set-up.
23: [----------] 1 test from CpuInfoTest
23: [ RUN ] CpuInfoTest.SupportLevel
23: [ OK ] CpuInfoTest.SupportLevel (2 ms)
23: [----------] 1 test from CpuInfoTest (2 ms total)
23:
23: [----------] 4 tests from HardwareTopologyTest
23: [ RUN ] HardwareTopologyTest.Execute
23: [ OK ] HardwareTopologyTest.Execute (35 ms)
23: [ RUN ] HardwareTopologyTest.HwlocExecute
23: [ OK ] HardwareTopologyTest.HwlocExecute (34 ms)
23: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
23: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (34 ms)
23: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
23: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (33 ms)
23: [----------] 4 tests from HardwareTopologyTest (136 ms total)
23:
23: [----------] 1 test from DevicesManagerTest
23: [ RUN ] DevicesManagerTest.Serialization
23: [ OK ] DevicesManagerTest.Serialization (0 ms)
23: [----------] 1 test from DevicesManagerTest (1 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 6 tests from 3 test cases ran. (140 ms total)
23: [ PASSED ] 6 tests.
23/65 Test #23: HardwareUnitTests ..................... Passed 0.20 sec
test 24
Start 24: MathUnitTests
24: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MathUnitTests.xml"
24: Test timeout computed to be: 30
24: [==========] Running 292 tests from 32 test cases.
24: [----------] Global test environment set-up.
24: [----------] 1 test from EmptyArrayRefWithPaddingTest
24: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
24: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
24: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total)
24:
24: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
24: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
24: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
24: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total)
24:
24: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
24: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
24: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
24: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
24: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
24: [----------] 2 tests from ArrayRefWithPaddingTest/0 (2 ms total)
24:
24: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
24: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
24: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
24: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
24: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (1 ms)
24: [----------] 2 tests from ArrayRefWithPaddingTest/1 (2 ms total)
24:
24: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
24: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
24: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
24: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
24: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
24: [----------] 2 tests from ArrayRefWithPaddingTest/2 (1 ms total)
24:
24: [----------] 11 tests from TranslateAndScaleTest
24: [ RUN ] TranslateAndScaleTest.identityTransformation
24: [ OK ] TranslateAndScaleTest.identityTransformation (1 ms)
24: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling
24: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation
24: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms)
24: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial
24: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms)
24: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector
24: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingIdentity
24: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingNonTrivial
24: [ OK ] TranslateAndScaleTest.scalingNonTrivial (1 ms)
24: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector
24: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero
24: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero
24: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector
24: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms)
24: [----------] 11 tests from TranslateAndScaleTest (5 ms total)
24:
24: [----------] 2 tests from AffineTransformationTest
24: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors
24: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms)
24: [ RUN ] AffineTransformationTest.applyTransformationToVectors
24: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms)
24: [----------] 2 tests from AffineTransformationTest (0 ms total)
24:
24: [----------] 12 tests from DensitySimilarityTest
24: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect
24: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (1 ms)
24: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect
24: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch
24: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms)
24: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch
24: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms)
24: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect
24: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero
24: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms)
24: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect
24: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect
24: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (23 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne
24: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (183 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated
24: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (194 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated
24: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (118 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect
24: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (1 ms)
24: [----------] 12 tests from DensitySimilarityTest (524 ms total)
24:
24: [----------] 6 tests from StructureSimilarityTest
24: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
24: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
24: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
24: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
24: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
24: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
24: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
24: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
24: [----------] 6 tests from StructureSimilarityTest (2 ms total)
24:
24: [----------] 8 tests from ExponentialMovingAverage
24: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero
24: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms)
24: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative
24: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (1 ms)
24: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue
24: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms)
24: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue
24: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms)
24: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly
24: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms)
24: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing
24: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms)
24: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect
24: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms)
24: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree
24: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms)
24: [----------] 8 tests from ExponentialMovingAverage (2 ms total)
24:
24: [----------] 21 tests from FunctionTest
24: [ RUN ] FunctionTest.StaticLog2
24: [ OK ] FunctionTest.StaticLog2 (0 ms)
24: [ RUN ] FunctionTest.Log2I32Bit
24: [ OK ] FunctionTest.Log2I32Bit (0 ms)
24: [ RUN ] FunctionTest.Log2I64Bit
24: [ OK ] FunctionTest.Log2I64Bit (1 ms)
24: [ RUN ] FunctionTest.GreatestCommonDivisor
24: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
24: [ RUN ] FunctionTest.InvsqrtFloat
24: [ OK ] FunctionTest.InvsqrtFloat (0 ms)
24: [ RUN ] FunctionTest.InvsqrtDouble
24: [ OK ] FunctionTest.InvsqrtDouble (0 ms)
24: [ RUN ] FunctionTest.InvsqrtInteger
24: [ OK ] FunctionTest.InvsqrtInteger (1 ms)
24: [ RUN ] FunctionTest.InvcbrtFloat
24: [ OK ] FunctionTest.InvcbrtFloat (1 ms)
24: [ RUN ] FunctionTest.InvcbrtDouble
24: [ OK ] FunctionTest.InvcbrtDouble (0 ms)
24: [ RUN ] FunctionTest.InvcbrtInteger
24: [ OK ] FunctionTest.InvcbrtInteger (1 ms)
24: [ RUN ] FunctionTest.SixthrootFloat
24: [ OK ] FunctionTest.SixthrootFloat (0 ms)
24: [ RUN ] FunctionTest.SixthrootDouble
24: [ OK ] FunctionTest.SixthrootDouble (1 ms)
24: [ RUN ] FunctionTest.SixthrootInteger
24: [ OK ] FunctionTest.SixthrootInteger (0 ms)
24: [ RUN ] FunctionTest.InvsixthrootFloat
24: [ OK ] FunctionTest.InvsixthrootFloat (1 ms)
24: [ RUN ] FunctionTest.InvsixthrootDouble
24: [ OK ] FunctionTest.InvsixthrootDouble (0 ms)
24: [ RUN ] FunctionTest.InvsixthrootInteger
24: [ OK ] FunctionTest.InvsixthrootInteger (0 ms)
24: [ RUN ] FunctionTest.Powers
24: [ OK ] FunctionTest.Powers (0 ms)
24: [ RUN ] FunctionTest.ErfInvFloat
24: [ OK ] FunctionTest.ErfInvFloat (1 ms)
24: [ RUN ] FunctionTest.ErfInvDouble
24: [ OK ] FunctionTest.ErfInvDouble (0 ms)
24: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
24: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms)
24: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
24: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms)
24: [----------] 21 tests from FunctionTest (14 ms total)
24:
24: [----------] 4 tests from GaussianOn1DLattice
24: [ RUN ] GaussianOn1DLattice.sumsCloseToOne
24: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms)
24: [ RUN ] GaussianOn1DLattice.isCorrect
24: [ OK ] GaussianOn1DLattice.isCorrect (0 ms)
24: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero
24: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms)
24: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange
24: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms)
24: [----------] 4 tests from GaussianOn1DLattice (0 ms total)
24:
24: [----------] 9 tests from GaussTransformTest
24: [ RUN ] GaussTransformTest.isZeroUponConstruction
24: [ OK ] GaussTransformTest.isZeroUponConstruction (1 ms)
24: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss
24: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms)
24: [ RUN ] GaussTransformTest.isZeroAfterSettingZero
24: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms)
24: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX
24: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms)
24: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY
24: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms)
24: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ
24: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms)
24: [ RUN ] GaussTransformTest.complementaryGaussAddToZero
24: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms)
24: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues
24: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms)
24: [ RUN ] GaussTransformTest.view
24: [ OK ] GaussTransformTest.view (1 ms)
24: [----------] 9 tests from GaussTransformTest (2 ms total)
24:
24: [----------] 3 tests from DensityFittingForce
24: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity
24: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms)
24: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections
24: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms)
24: [ RUN ] DensityFittingForce.pullsTowardsDerivative
24: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms)
24: [----------] 3 tests from DensityFittingForce (0 ms total)
24:
24: [----------] 2 tests from InvertMatrixTest
24: [ RUN ] InvertMatrixTest.IdentityIsImpotent
24: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
24: [ RUN ] InvertMatrixTest.ComputesInverse
24: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
24: [----------] 2 tests from InvertMatrixTest (0 ms total)
24:
24: [----------] 2 tests from InvertBoxMatrixTest
24: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
24: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
24: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
24: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
24: [----------] 2 tests from InvertBoxMatrixTest (0 ms total)
24:
24: [----------] 17 tests from MatrixTest
24: [ RUN ] MatrixTest.canSetFromArray
24: [ OK ] MatrixTest.canSetFromArray (1 ms)
24: [ RUN ] MatrixTest.canSetStaticallyFromList
24: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms)
24: [ RUN ] MatrixTest.canConstructAndFill
24: [ OK ] MatrixTest.canConstructAndFill (0 ms)
24: [ RUN ] MatrixTest.canSetValues
24: [ OK ] MatrixTest.canSetValues (0 ms)
24: [ RUN ] MatrixTest.canCopyAssign
24: [ OK ] MatrixTest.canCopyAssign (0 ms)
24: [ RUN ] MatrixTest.canSwap
24: [ OK ] MatrixTest.canSwap (0 ms)
24: [ RUN ] MatrixTest.staticMultiDimArrayExtent
24: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms)
24: [ RUN ] MatrixTest.determinantWorks
24: [ OK ] MatrixTest.determinantWorks (0 ms)
24: [ RUN ] MatrixTest.noninvertableDeterminantIsZero
24: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms)
24: [ RUN ] MatrixTest.determinantOfDiagonalMatrix
24: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms)
24: [ RUN ] MatrixTest.traceWorks
24: [ OK ] MatrixTest.traceWorks (0 ms)
24: [ RUN ] MatrixTest.transposeWorks
24: [ OK ] MatrixTest.transposeWorks (0 ms)
24: [ RUN ] MatrixTest.transposeOfSymmetricMatrix
24: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms)
24: [ RUN ] MatrixTest.canCreateFromLegacyMatrix
24: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms)
24: [ RUN ] MatrixTest.canFillLegacyMatrix
24: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms)
24: [ RUN ] MatrixTest.IdentityMatrix
24: [ OK ] MatrixTest.IdentityMatrix (0 ms)
24: [ RUN ] MatrixTest.MatrixVectorMultiplication
24: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms)
24: [----------] 17 tests from MatrixTest (2 ms total)
24:
24: [----------] 25 tests from MultiDimArrayTest
24: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic
24: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic
24: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSetValuesInStatic
24: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic
24: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveConstructStatic
24: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic
24: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveAssignStatic
24: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic
24: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyConstructStatic
24: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic
24: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyAssignStatic
24: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic
24: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSwapStatic
24: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSwapDynamic
24: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent
24: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms)
24: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent
24: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms)
24: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent
24: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms)
24: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue
24: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms)
24: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray
24: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms)
24: [ RUN ] MultiDimArrayTest.conversionToView
24: [ OK ] MultiDimArrayTest.conversionToView (0 ms)
24: [ RUN ] MultiDimArrayTest.conversionToConstView
24: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms)
24: [ RUN ] MultiDimArrayTest.viewBegin
24: [ OK ] MultiDimArrayTest.viewBegin (0 ms)
24: [ RUN ] MultiDimArrayTest.viewEnd
24: [ OK ] MultiDimArrayTest.viewEnd (0 ms)
24: [ RUN ] MultiDimArrayTest.constViewConstBegin
24: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms)
24: [ RUN ] MultiDimArrayTest.constViewConstEnd
24: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms)
24: [----------] 25 tests from MultiDimArrayTest (1 ms total)
24:
24: [----------] 4 tests from MultiDimArrayToMdSpanTest
24: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms)
24: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms)
24: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms)
24: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms)
24: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total)
24:
24: [----------] 9 tests from NelderMeadSimplexTest
24: [ RUN ] NelderMeadSimplexTest.BestVertex
24: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms)
24: [ RUN ] NelderMeadSimplexTest.WorstVertex
24: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms)
24: [ RUN ] NelderMeadSimplexTest.SecondWorstValue
24: [ OK ] NelderMeadSimplexTest.SecondWorstValue (1 ms)
24: [ RUN ] NelderMeadSimplexTest.ReflectionPoint
24: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms)
24: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint
24: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms)
24: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint
24: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms)
24: [ RUN ] NelderMeadSimplexTest.SwapOutWorst
24: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms)
24: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest
24: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms)
24: [ RUN ] NelderMeadSimplexTest.OrientedLength
24: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms)
24: [----------] 9 tests from NelderMeadSimplexTest (1 ms total)
24:
24: [----------] 2 tests from NelderMead
24: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly
24: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (1 ms)
24: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly
24: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (1 ms)
24: [----------] 2 tests from NelderMead (2 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
24: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ResizeWorks
24: [ OK ] PaddedVectorTest/0.ResizeWorks (1 ms)
24: [ RUN ] PaddedVectorTest/0.ReserveWorks
24: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/0.CanCopyAssign
24: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/0.CanMoveAssign
24: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/0.CanSwap
24: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/0 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
24: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ResizeWorks
24: [ OK ] PaddedVectorTest/1.ResizeWorks (1 ms)
24: [ RUN ] PaddedVectorTest/1.ReserveWorks
24: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/1.CanCopyAssign
24: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/1.CanMoveAssign
24: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/1.CanSwap
24: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/1 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
24: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ResizeWorks
24: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ReserveWorks
24: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (1 ms)
24: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/2.CanCopyAssign
24: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/2.CanMoveAssign
24: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/2.CanSwap
24: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/2 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
24: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ResizeWorks
24: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ReserveWorks
24: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/3.CanCopyAssign
24: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/3.CanMoveAssign
24: [ OK ] PaddedVectorTest/3.CanMoveAssign (1 ms)
24: [ RUN ] PaddedVectorTest/3.CanSwap
24: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/3 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
24: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ResizeWorks
24: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ReserveWorks
24: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/4.CanCopyAssign
24: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/4.CanMoveAssign
24: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/4.CanSwap
24: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/4 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ResizeWorks
24: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ReserveWorks
24: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (1 ms)
24: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/5.CanCopyAssign
24: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/5.CanMoveAssign
24: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/5.CanSwap
24: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/5 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ResizeWorks
24: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ReserveWorks
24: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (1 ms)
24: [ RUN ] PaddedVectorTest/6.CanCopyAssign
24: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/6.CanMoveAssign
24: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/6.CanSwap
24: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/6 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ResizeWorks
24: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ReserveWorks
24: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/7.CanCopyAssign
24: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/7.CanMoveAssign
24: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/7.CanSwap
24: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/7 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ResizeWorks
24: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ReserveWorks
24: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/8.CanCopyAssign
24: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/8.CanMoveAssign
24: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/8.CanSwap
24: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/8 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ResizeWorks
24: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ReserveWorks
24: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/9.CanCopyAssign
24: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/9.CanMoveAssign
24: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/9.CanSwap
24: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/9 (1 ms total)
24:
24: [----------] 37 tests from RVecTest
24: [ RUN ] RVecTest.CanBeStoredInVector
24: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
24: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
24: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
24: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
24: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
24: [ RUN ] RVecTest.WorksAsMutable_rvec
24: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
24: [ RUN ] RVecTest.WorksAs_rvec_Array
24: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
24: [ RUN ] RVecTest.CanAddRVecToRvec
24: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
24: [ RUN ] RVecTest.CanAddAssignRVecToRvec
24: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
24: [ RUN ] RVecTest.CanSubtractRVecFromRvec
24: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
24: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
24: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (1 ms)
24: [ RUN ] RVecTest.CanDotProductRVecByRvec
24: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
24: [ RUN ] RVecTest.CanCrossProductRVecByRvec
24: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
24: [ RUN ] RVecTest.CanDivideRVecInplace
24: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
24: [ RUN ] RVecTest.CanScaleRVec
24: [ OK ] RVecTest.CanScaleRVec (0 ms)
24: [ RUN ] RVecTest.CanDivideRVec
24: [ OK ] RVecTest.CanDivideRVec (0 ms)
24: [ RUN ] RVecTest.CanDoUnitvFromRVec
24: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
24: [ RUN ] RVecTest.CanSqLengthOfRVec
24: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanLengthOfRVec
24: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanCastToRVec
24: [ OK ] RVecTest.CanCastToRVec (0 ms)
24: [ RUN ] RVecTest.CanCastToDVec
24: [ OK ] RVecTest.CanCastToDVec (0 ms)
24: [ RUN ] RVecTest.CanLeftScalarMultiply
24: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
24: [ RUN ] RVecTest.CanRightScalarMultiply
24: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
24: [ RUN ] RVecTest.CanGetUnitvFromRVec
24: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
24: [ RUN ] RVecTest.CanGetSqLengthOfRVec
24: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanGetLengthOfRVec
24: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanDoCrossProductOfRVec
24: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
24: [ RUN ] RVecTest.CanDoDotProductOfRVec
24: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
24: [ RUN ] RVecTest.CanScaleByVector
24: [ OK ] RVecTest.CanScaleByVector (0 ms)
24: [ RUN ] RVecTest.asIVec
24: [ OK ] RVecTest.asIVec (0 ms)
24: [ RUN ] RVecTest.elementWiseMin
24: [ OK ] RVecTest.elementWiseMin (0 ms)
24: [ RUN ] RVecTest.elementWiseMax
24: [ OK ] RVecTest.elementWiseMax (0 ms)
24: [ RUN ] RVecTest.WorksAs_dvec_Reference
24: [ OK ] RVecTest.WorksAs_dvec_Reference (1 ms)
24: [ RUN ] RVecTest.WorksAs_ivec_Reference
24: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
24: [ RUN ] RVecTest.WorksAs_rvec_Reference
24: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
24: [ RUN ] RVecTest.CopyConstructorWorks
24: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
24: [ RUN ] RVecTest.CopyAssignmentWorks
24: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
24: [ RUN ] RVecTest.MoveConstructorWorks
24: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
24: [ RUN ] RVecTest.MoveAssignmentWorks
24: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
24: [----------] 37 tests from RVecTest (2 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 292 tests from 32 test cases ran. (581 ms total)
24: [ PASSED ] 292 tests.
24/65 Test #24: MathUnitTests ......................... Passed 0.70 sec
test 25
Start 25: MdrunUtilityUnitTests
25: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml"
25: Test timeout computed to be: 30
25: [==========] Running 17 tests from 1 test case.
25: [----------] Global test environment set-up.
25: [----------] 17 tests from ThreadAffinityTest
25: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
25: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
25: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (1 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (1 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
25: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
25: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
25: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms)
25: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
25: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
25: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
25: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (2 ms)
25: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
25: NOTE: Affinity setting failed.
25: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
25: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
25: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (2 ms)
25: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
25: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (1 ms)
25: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
25: NOTE: Affinity setting for 1/2 threads failed.
25: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (2 ms)
25: [----------] 17 tests from ThreadAffinityTest (20 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 17 tests from 1 test case ran. (22 ms total)
25: [ PASSED ] 17 tests.
25/65 Test #25: MdrunUtilityUnitTests ................. Passed 0.09 sec
test 26
Start 26: MdrunUtilityMpiUnitTests
26: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
26: Test timeout computed to be: 30
26: [==========] Running 13 tests from 2 test cases.
26: [----------] Global test environment set-up.
26: [----------] 6 tests from ThreadAffinityMultiRankTest
26: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
26: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (10 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
26: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (6 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
26: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (5 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
26: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (1 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
26: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (5 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
26: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (3 ms)
26: [----------] 6 tests from ThreadAffinityMultiRankTest (31 ms total)
26:
26: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (4 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (3 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (4 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (4 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (4 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (5 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (4 ms)
26: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (31 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 13 tests from 2 test cases ran. (63 ms total)
26: [ PASSED ] 13 tests.
26/65 Test #26: MdrunUtilityMpiUnitTests .............. Passed 0.13 sec
test 27
Start 27: MDSpanTests
27: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MDSpanTests.xml"
27: Test timeout computed to be: 30
27: [==========] Running 32 tests from 7 test cases.
27: [----------] Global test environment set-up.
27: [----------] 4 tests from BasicAccessorPolicy
27: [ RUN ] BasicAccessorPolicy.Decay
27: [ OK ] BasicAccessorPolicy.Decay (0 ms)
27: [ RUN ] BasicAccessorPolicy.Access
27: [ OK ] BasicAccessorPolicy.Access (0 ms)
27: [ RUN ] BasicAccessorPolicy.Offset
27: [ OK ] BasicAccessorPolicy.Offset (0 ms)
27: [ RUN ] BasicAccessorPolicy.CopyAccessor
27: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms)
27: [----------] 4 tests from BasicAccessorPolicy (1 ms total)
27:
27: [----------] 4 tests from ExtentsTest
27: [ RUN ] ExtentsTest.Construction
27: [ OK ] ExtentsTest.Construction (0 ms)
27: [ RUN ] ExtentsTest.PurelyStatic
27: [ OK ] ExtentsTest.PurelyStatic (0 ms)
27: [ RUN ] ExtentsTest.RankNought
27: [ OK ] ExtentsTest.RankNought (0 ms)
27: [ RUN ] ExtentsTest.Assignment
27: [ OK ] ExtentsTest.Assignment (0 ms)
27: [----------] 4 tests from ExtentsTest (1 ms total)
27:
27: [----------] 8 tests from MdSpanExtension
27: [ RUN ] MdSpanExtension.SlicingAllStatic
27: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms)
27: [ RUN ] MdSpanExtension.SlicingDynamic
27: [ OK ] MdSpanExtension.SlicingDynamic (0 ms)
27: [ RUN ] MdSpanExtension.SlicingAllStatic3D
27: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms)
27: [ RUN ] MdSpanExtension.SlicingEqualsView3D
27: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms)
27: [ RUN ] MdSpanExtension.additionWorks
27: [ OK ] MdSpanExtension.additionWorks (0 ms)
27: [ RUN ] MdSpanExtension.subtractionWorks
27: [ OK ] MdSpanExtension.subtractionWorks (0 ms)
27: [ RUN ] MdSpanExtension.multiplicationWorks
27: [ OK ] MdSpanExtension.multiplicationWorks (0 ms)
27: [ RUN ] MdSpanExtension.divisionWorks
27: [ OK ] MdSpanExtension.divisionWorks (0 ms)
27: [----------] 8 tests from MdSpanExtension (2 ms total)
27:
27: [----------] 3 tests from LayoutTests
27: [ RUN ] LayoutTests.LayoutRightConstruction
27: [ OK ] LayoutTests.LayoutRightConstruction (0 ms)
27: [ RUN ] LayoutTests.LayoutRightProperties
27: [ OK ] LayoutTests.LayoutRightProperties (0 ms)
27: [ RUN ] LayoutTests.LayoutRightOperator
27: [ OK ] LayoutTests.LayoutRightOperator (0 ms)
27: [----------] 3 tests from LayoutTests (1 ms total)
27:
27: [----------] 1 test from MdSpanTest
27: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly
27: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms)
27: [----------] 1 test from MdSpanTest (1 ms total)
27:
27: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan<int, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<int> >
27: [ RUN ] MdSpanTest/0.Rank
27: [ OK ] MdSpanTest/0.Rank (0 ms)
27: [ RUN ] MdSpanTest/0.DynamicRank
27: [ OK ] MdSpanTest/0.DynamicRank (0 ms)
27: [ RUN ] MdSpanTest/0.Extents
27: [ OK ] MdSpanTest/0.Extents (1 ms)
27: [ RUN ] MdSpanTest/0.Strides
27: [ OK ] MdSpanTest/0.Strides (0 ms)
27: [ RUN ] MdSpanTest/0.Properties
27: [ OK ] MdSpanTest/0.Properties (0 ms)
27: [ RUN ] MdSpanTest/0.Operator
27: [ OK ] MdSpanTest/0.Operator (0 ms)
27: [----------] 6 tests from MdSpanTest/0 (1 ms total)
27:
27: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan<float, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<float> >
27: [ RUN ] MdSpanTest/1.Rank
27: [ OK ] MdSpanTest/1.Rank (0 ms)
27: [ RUN ] MdSpanTest/1.DynamicRank
27: [ OK ] MdSpanTest/1.DynamicRank (0 ms)
27: [ RUN ] MdSpanTest/1.Extents
27: [ OK ] MdSpanTest/1.Extents (0 ms)
27: [ RUN ] MdSpanTest/1.Strides
27: [ OK ] MdSpanTest/1.Strides (0 ms)
27: [ RUN ] MdSpanTest/1.Properties
27: [ OK ] MdSpanTest/1.Properties (0 ms)
27: [ RUN ] MdSpanTest/1.Operator
27: [ OK ] MdSpanTest/1.Operator (0 ms)
27: [----------] 6 tests from MdSpanTest/1 (1 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 32 tests from 7 test cases ran. (12 ms total)
27: [ PASSED ] 32 tests.
27/65 Test #27: MDSpanTests ........................... Passed 0.08 sec
test 28
Start 28: MdtypesUnitTest
28: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdtypes-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdtypesUnitTest.xml"
28: Test timeout computed to be: 30
28: [==========] Running 9 tests from 2 test cases.
28: [----------] Global test environment set-up.
28: [----------] 2 tests from CheckpointDataTest
28: [ RUN ] CheckpointDataTest.SingleDataTest
28: [ OK ] CheckpointDataTest.SingleDataTest (9 ms)
28: [ RUN ] CheckpointDataTest.MultiDataTest
28: [ OK ] CheckpointDataTest.MultiDataTest (61 ms)
28: [----------] 2 tests from CheckpointDataTest (72 ms total)
28:
28: [----------] 7 tests from ForceBuffers
28: [ RUN ] ForceBuffers.ConstructsUnpinned
28: [ OK ] ForceBuffers.ConstructsUnpinned (1 ms)
28: [ RUN ] ForceBuffers.ConstructsPinned
28: [ OK ] ForceBuffers.ConstructsPinned (0 ms)
28: [ RUN ] ForceBuffers.ConstructsEmpty
28: [ OK ] ForceBuffers.ConstructsEmpty (0 ms)
28: [ RUN ] ForceBuffers.ResizeWorks
28: [ OK ] ForceBuffers.ResizeWorks (0 ms)
28: [ RUN ] ForceBuffers.PaddingWorks
28: [ OK ] ForceBuffers.PaddingWorks (0 ms)
28: [ RUN ] ForceBuffers.CopyWorks
28: [ OK ] ForceBuffers.CopyWorks (0 ms)
28: [ RUN ] ForceBuffers.CopyDoesNotPin
28: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms)
28: [----------] 7 tests from ForceBuffers (2 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 9 tests from 2 test cases ran. (76 ms total)
28: [ PASSED ] 9 tests.
28/65 Test #28: MdtypesUnitTest ....................... Passed 0.14 sec
test 29
Start 29: OnlineHelpUnitTests
29: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml"
29: Test timeout computed to be: 30
29: [==========] Running 22 tests from 4 test cases.
29: [----------] Global test environment set-up.
29: [----------] 6 tests from TextTableFormatterTest
29: [ RUN ] TextTableFormatterTest.HandlesBasicCase
29: [ OK ] TextTableFormatterTest.HandlesBasicCase (41 ms)
29: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
29: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (1 ms)
29: [ RUN ] TextTableFormatterTest.HandlesIndentation
29: [ OK ] TextTableFormatterTest.HandlesIndentation (1 ms)
29: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
29: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (1 ms)
29: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
29: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms)
29: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
29: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms)
29: [----------] 6 tests from TextTableFormatterTest (46 ms total)
29:
29: [----------] 3 tests from HelpManagerTest
29: [ RUN ] HelpManagerTest.HandlesRootTopic
29: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms)
29: [ RUN ] HelpManagerTest.HandlesSubTopics
29: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms)
29: [ RUN ] HelpManagerTest.HandlesInvalidTopics
29: [ OK ] HelpManagerTest.HandlesInvalidTopics (1 ms)
29: [----------] 3 tests from HelpManagerTest (2 ms total)
29:
29: [----------] 2 tests from HelpTopicFormattingTest
29: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
29: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms)
29: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
29: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms)
29: [----------] 2 tests from HelpTopicFormattingTest (2 ms total)
29:
29: [----------] 11 tests from HelpWriterContextTest
29: [ RUN ] HelpWriterContextTest.FormatsParagraphs
29: [ OK ] HelpWriterContextTest.FormatsParagraphs (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
29: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms)
29: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
29: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsLiteralText
29: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
29: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
29: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsBulletList
29: [ OK ] HelpWriterContextTest.FormatsBulletList (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
29: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
29: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsGridTable
29: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsTitles
29: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms)
29: [----------] 11 tests from HelpWriterContextTest (9 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 22 tests from 4 test cases ran. (63 ms total)
29: [ PASSED ] 22 tests.
29/65 Test #29: OnlineHelpUnitTests ................... Passed 0.13 sec
test 30
Start 30: OptionsUnitTests
30: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml"
30: Test timeout computed to be: 30
30: [==========] Running 111 tests from 18 test cases.
30: [----------] Global test environment set-up.
30: [----------] 5 tests from AbstractOptionStorageTest
30: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
30: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (2 ms)
30: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
30: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms)
30: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
30: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (1 ms)
30: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
30: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (2 ms)
30: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
30: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (1 ms)
30: [----------] 5 tests from AbstractOptionStorageTest (8 ms total)
30:
30: [----------] 10 tests from FileNameOptionTest
30: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
30: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
30: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
30: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
30: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (1 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
30: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
30: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
30: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
30: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (1 ms)
30: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
30: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension
30: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue
30: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms)
30: [----------] 10 tests from FileNameOptionTest (2 ms total)
30:
30: [----------] 15 tests from FileNameOptionManagerTest
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
30: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (1 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (1 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
30: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
30: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
30: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (1 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (1 ms)
30: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
30: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (1 ms)
30: [----------] 15 tests from FileNameOptionManagerTest (5 ms total)
30:
30: [----------] 1 test from OptionsTest
30: [ RUN ] OptionsTest.FailsOnNonsafeStorage
30: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms)
30: [----------] 1 test from OptionsTest (0 ms total)
30:
30: [----------] 9 tests from OptionsAssignerTest
30: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
30: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
30: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
30: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
30: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesMissingValue
30: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesExtraValue
30: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesGroups
30: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesSections
30: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
30: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
30: [----------] 9 tests from OptionsAssignerTest (1 ms total)
30:
30: [----------] 4 tests from OptionsAssignerBooleanTest
30: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
30: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (1 ms)
30: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
30: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
30: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
30: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
30: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
30: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms)
30: [----------] 4 tests from OptionsAssignerBooleanTest (1 ms total)
30:
30: [----------] 13 tests from OptionsAssignerIntegerTest
30: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
30: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
30: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
30: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
30: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
30: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
30: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
30: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
30: [----------] 13 tests from OptionsAssignerIntegerTest (2 ms total)
30:
30: [----------] 5 tests from OptionsAssignerDoubleTest
30: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
30: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
30: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
30: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
30: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
30: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
30: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total)
30:
30: [----------] 9 tests from OptionsAssignerStringTest
30: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
30: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
30: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
30: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
30: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
30: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
30: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
30: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
30: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
30: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
30: [----------] 9 tests from OptionsAssignerStringTest (0 ms total)
30:
30: [----------] 6 tests from OptionsAssignerEnumTest
30: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
30: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
30: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (1 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
30: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
30: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
30: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
30: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
30: [----------] 6 tests from OptionsAssignerEnumTest (1 ms total)
30:
30: [----------] 8 tests from RepeatingOptionSectionTest
30: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
30: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
30: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
30: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
30: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
30: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
30: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
30: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
30: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (1 ms)
30: [----------] 8 tests from RepeatingOptionSectionTest (1 ms total)
30:
30: [----------] 1 test from TimeUnitManagerTest
30: [ RUN ] TimeUnitManagerTest.BasicOperations
30: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
30: [----------] 1 test from TimeUnitManagerTest (0 ms total)
30:
30: [----------] 4 tests from TimeUnitBehaviorTest
30: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
30: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
30: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
30: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
30: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
30: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
30: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
30: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms)
30: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total)
30:
30: [----------] 2 tests from TreeValueSupportAssignTest
30: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
30: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (1 ms)
30: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
30: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
30: [----------] 2 tests from TreeValueSupportAssignTest (1 ms total)
30:
30: [----------] 1 test from TreeValueSupportAssignErrorTest
30: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
30: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (1 ms)
30: [----------] 1 test from TreeValueSupportAssignErrorTest (1 ms total)
30:
30: [----------] 5 tests from TreeValueSupportCheckTest
30: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
30: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
30: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (1 ms)
30: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
30: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
30: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
30: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
30: [----------] 5 tests from TreeValueSupportCheckTest (1 ms total)
30:
30: [----------] 6 tests from TreeValueSupportAdjustTest
30: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
30: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (6 ms)
30: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
30: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (1 ms)
30: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
30: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
30: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
30: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (1 ms)
30: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
30: [ OK ] TreeValueSupportAdjustTest.OrdersValues (1 ms)
30: [----------] 6 tests from TreeValueSupportAdjustTest (10 ms total)
30:
30: [----------] 7 tests from TreeValueSupportTest
30: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
30: [ OK ] TreeValueSupportTest.SupportsBooleanOption (6 ms)
30: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
30: [ OK ] TreeValueSupportTest.SupportsIntegerOption (1 ms)
30: [ RUN ] TreeValueSupportTest.SupportsInt64Option
30: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms)
30: [ RUN ] TreeValueSupportTest.SupportsStringOption
30: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsFloatOption
30: [ OK ] TreeValueSupportTest.SupportsFloatOption (1 ms)
30: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
30: [ OK ] TreeValueSupportTest.SupportsDoubleOption (1 ms)
30: [ RUN ] TreeValueSupportTest.SupportsEnumOption
30: [ OK ] TreeValueSupportTest.SupportsEnumOption (1 ms)
30: [----------] 7 tests from TreeValueSupportTest (11 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 111 tests from 18 test cases ran. (53 ms total)
30: [ PASSED ] 111 tests.
30/65 Test #30: OptionsUnitTests ...................... Passed 0.13 sec
test 31
Start 31: PbcutilUnitTest
31: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml"
31: Test timeout computed to be: 30
31: [==========] Running 33 tests from 5 test cases.
31: [----------] Global test environment set-up.
31: [----------] 1 test from ShiftTest
31: [ RUN ] ShiftTest.CoordinateShiftWorks
31: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms)
31: [----------] 1 test from ShiftTest (0 ms total)
31:
31: [----------] 2 tests from MShift
31: [ RUN ] MShift.shiftsAndUnshifts
31: [ OK ] MShift.shiftsAndUnshifts (1 ms)
31: [ RUN ] MShift.shiftsAndUnshiftsSelf
31: [ OK ] MShift.shiftsAndUnshiftsSelf (1 ms)
31: [----------] 2 tests from MShift (2 ms total)
31:
31: [----------] 1 test from PbcTest
31: [ RUN ] PbcTest.CalcShiftsWorks
31: [ OK ] PbcTest.CalcShiftsWorks (34 ms)
31: [----------] 1 test from PbcTest (34 ms total)
31:
31: [----------] 2 tests from PbcEnumsTest
31: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect
31: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms)
31: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect
31: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms)
31: [----------] 2 tests from PbcEnumsTest (0 ms total)
31:
31: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (8 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (2 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (1 ms)
31: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (56 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 33 tests from 5 test cases ran. (92 ms total)
31: [ PASSED ] 33 tests.
31/65 Test #31: PbcutilUnitTest ....................... Passed 0.16 sec
test 32
Start 32: RandomUnitTests
32: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/RandomUnitTests.xml"
32: Test timeout computed to be: 30
32: [==========] Running 44 tests from 10 test cases.
32: [----------] Global test environment set-up.
32: [----------] 4 tests from ExponentialDistributionTest
32: [ RUN ] ExponentialDistributionTest.Output
32: [ OK ] ExponentialDistributionTest.Output (24 ms)
32: [ RUN ] ExponentialDistributionTest.Logical
32: [ OK ] ExponentialDistributionTest.Logical (0 ms)
32: [ RUN ] ExponentialDistributionTest.Reset
32: [ OK ] ExponentialDistributionTest.Reset (0 ms)
32: [ RUN ] ExponentialDistributionTest.AltParam
32: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from ExponentialDistributionTest (24 ms total)
32:
32: [----------] 4 tests from GammaDistributionTest
32: [ RUN ] GammaDistributionTest.Output
32: [ OK ] GammaDistributionTest.Output (1 ms)
32: [ RUN ] GammaDistributionTest.Logical
32: [ OK ] GammaDistributionTest.Logical (0 ms)
32: [ RUN ] GammaDistributionTest.Reset
32: [ OK ] GammaDistributionTest.Reset (0 ms)
32: [ RUN ] GammaDistributionTest.AltParam
32: [ OK ] GammaDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from GammaDistributionTest (2 ms total)
32:
32: [----------] 4 tests from NormalDistributionTest
32: [ RUN ] NormalDistributionTest.Output
32: [ OK ] NormalDistributionTest.Output (0 ms)
32: [ RUN ] NormalDistributionTest.Logical
32: [ OK ] NormalDistributionTest.Logical (0 ms)
32: [ RUN ] NormalDistributionTest.Reset
32: [ OK ] NormalDistributionTest.Reset (0 ms)
32: [ RUN ] NormalDistributionTest.AltParam
32: [ OK ] NormalDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from NormalDistributionTest (0 ms total)
32:
32: [----------] 1 test from SeedTest
32: [ RUN ] SeedTest.makeRandomSeed
32: [ OK ] SeedTest.makeRandomSeed (1 ms)
32: [----------] 1 test from SeedTest (1 ms total)
32:
32: [----------] 6 tests from TabulatedNormalDistributionTest
32: [ RUN ] TabulatedNormalDistributionTest.Output14
32: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.Output16
32: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
32: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (1 ms)
32: [ RUN ] TabulatedNormalDistributionTest.Logical
32: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.Reset
32: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.AltParam
32: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
32: [----------] 6 tests from TabulatedNormalDistributionTest (2 ms total)
32:
32: [----------] 1 test from TabulatedNormalDistributionTableTest
32: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
32: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (8 ms)
32: [----------] 1 test from TabulatedNormalDistributionTableTest (8 ms total)
32:
32: [----------] 6 tests from ThreeFry2x64Test
32: [ RUN ] ThreeFry2x64Test.Logical
32: [ OK ] ThreeFry2x64Test.Logical (0 ms)
32: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
32: [ OK ] ThreeFry2x64Test.InternalCounterSequence (1 ms)
32: [ RUN ] ThreeFry2x64Test.Reseed
32: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
32: [ RUN ] ThreeFry2x64Test.Discard
32: [ OK ] ThreeFry2x64Test.Discard (0 ms)
32: [ RUN ] ThreeFry2x64Test.InvalidCounter
32: [ OK ] ThreeFry2x64Test.InvalidCounter (1 ms)
32: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
32: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
32: [----------] 6 tests from ThreeFry2x64Test (2 ms total)
32:
32: [----------] 4 tests from UniformIntDistributionTest
32: [ RUN ] UniformIntDistributionTest.Output
32: [ OK ] UniformIntDistributionTest.Output (0 ms)
32: [ RUN ] UniformIntDistributionTest.Logical
32: [ OK ] UniformIntDistributionTest.Logical (1 ms)
32: [ RUN ] UniformIntDistributionTest.Reset
32: [ OK ] UniformIntDistributionTest.Reset (0 ms)
32: [ RUN ] UniformIntDistributionTest.AltParam
32: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from UniformIntDistributionTest (1 ms total)
32:
32: [----------] 5 tests from UniformRealDistributionTest
32: [ RUN ] UniformRealDistributionTest.GenerateCanonical
32: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms)
32: [ RUN ] UniformRealDistributionTest.Output
32: [ OK ] UniformRealDistributionTest.Output (1 ms)
32: [ RUN ] UniformRealDistributionTest.Logical
32: [ OK ] UniformRealDistributionTest.Logical (0 ms)
32: [ RUN ] UniformRealDistributionTest.Reset
32: [ OK ] UniformRealDistributionTest.Reset (0 ms)
32: [ RUN ] UniformRealDistributionTest.AltParam
32: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
32: [----------] 5 tests from UniformRealDistributionTest (1 ms total)
32:
32: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (1 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (1 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (1 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms)
32: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (4 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 44 tests from 10 test cases ran. (45 ms total)
32: [ PASSED ] 44 tests.
32/65 Test #32: RandomUnitTests ....................... Passed 0.14 sec
test 33
Start 33: RestraintTests
33: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/RestraintTests.xml"
33: Test timeout computed to be: 30
33: [==========] Running 1 test from 1 test case.
33: [----------] Global test environment set-up.
33: [----------] 1 test from RestraintManager
33: [ RUN ] RestraintManager.restraintList
33: [ OK ] RestraintManager.restraintList (0 ms)
33: [----------] 1 test from RestraintManager (0 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 1 test from 1 test case ran. (1 ms total)
33: [ PASSED ] 1 test.
33/65 Test #33: RestraintTests ........................ Passed 0.06 sec
test 34
Start 34: TableUnitTests
34: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TableUnitTests.xml"
34: Test timeout computed to be: 30
34: [==========] Running 16 tests from 2 test cases.
34: [----------] Global test environment set-up.
34: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
34: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
34: [ OK ] SplineTableTest/0.HandlesIncorrectInput (7 ms)
34: [ RUN ] SplineTableTest/0.Sinc
34: [ OK ] SplineTableTest/0.Sinc (4 ms)
34: [ RUN ] SplineTableTest/0.LJ12
34: [ OK ] SplineTableTest/0.LJ12 (89 ms)
34: [ RUN ] SplineTableTest/0.PmeCorrection
34: [ OK ] SplineTableTest/0.PmeCorrection (7 ms)
34: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
34: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (2 ms)
34: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
34: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (6 ms)
34: [ RUN ] SplineTableTest/0.TwoFunctions
34: [ OK ] SplineTableTest/0.TwoFunctions (179 ms)
34: [ RUN ] SplineTableTest/0.ThreeFunctions
34: [ OK ] SplineTableTest/0.ThreeFunctions (222 ms)
34: [----------] 8 tests from SplineTableTest/0 (521 ms total)
34:
34: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
34: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
34: [ OK ] SplineTableTest/1.HandlesIncorrectInput (7 ms)
34: [ RUN ] SplineTableTest/1.Sinc
34: [ OK ] SplineTableTest/1.Sinc (10 ms)
34: [ RUN ] SplineTableTest/1.LJ12
34: [ OK ] SplineTableTest/1.LJ12 (318 ms)
34: [ RUN ] SplineTableTest/1.PmeCorrection
34: [ OK ] SplineTableTest/1.PmeCorrection (7 ms)
34: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
34: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (2 ms)
34: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
34: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (6 ms)
34: [ RUN ] SplineTableTest/1.TwoFunctions
34: [ OK ] SplineTableTest/1.TwoFunctions (447 ms)
34: [ RUN ] SplineTableTest/1.ThreeFunctions
34: [ OK ] SplineTableTest/1.ThreeFunctions (538 ms)
34: [----------] 8 tests from SplineTableTest/1 (1337 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 16 tests from 2 test cases ran. (1859 ms total)
34: [ PASSED ] 16 tests.
34/65 Test #34: TableUnitTests ........................ Passed 1.93 sec
test 35
Start 35: TaskAssignmentUnitTests
35: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml"
35: Test timeout computed to be: 30
35: [==========] Running 3 tests from 2 test cases.
35: [----------] Global test environment set-up.
35: [----------] 2 tests from UserTaskAssignmentStringHandlingTest
35: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork
35: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (1 ms)
35: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid
35: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms)
35: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (1 ms total)
35:
35: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest
35: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow
35: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (2 ms)
35: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (2 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 3 tests from 2 test cases ran. (4 ms total)
35: [ PASSED ] 3 tests.
35/65 Test #35: TaskAssignmentUnitTests ............... Passed 0.07 sec
test 36
Start 36: TopologyTest
36: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/topology-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TopologyTest.xml"
36: Test timeout computed to be: 30
36: [==========] Running 31 tests from 5 test cases.
36: [----------] Global test environment set-up.
36: [----------] 3 tests from ExclusionBlockTest
36: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks
36: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms)
36: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka
36: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms)
36: [ RUN ] ExclusionBlockTest.MergeExclusions
36: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms)
36: [----------] 3 tests from ExclusionBlockTest (1 ms total)
36:
36: [----------] 6 tests from InteractionListTest
36: [ RUN ] InteractionListTest.EmptyWorks
36: [ OK ] InteractionListTest.EmptyWorks (0 ms)
36: [ RUN ] InteractionListTest.CanAddInteractionArray
36: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms)
36: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms
36: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms)
36: [ RUN ] InteractionListTest.CanAddInteractionPointer
36: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms)
36: [ RUN ] InteractionListTest.CanAddListToOtherList
36: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms)
36: [ RUN ] InteractionListTest.ClearingWorks
36: [ OK ] InteractionListTest.ClearingWorks (0 ms)
36: [----------] 6 tests from InteractionListTest (1 ms total)
36:
36: [----------] 3 tests from MtopTest
36: [ RUN ] MtopTest.RangeBasedLoop
36: [ OK ] MtopTest.RangeBasedLoop (0 ms)
36: [ RUN ] MtopTest.Operators
36: [ OK ] MtopTest.Operators (0 ms)
36: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms
36: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms)
36: [----------] 3 tests from MtopTest (0 ms total)
36:
36: [----------] 13 tests from StringTableTest
36: [ RUN ] StringTableTest.AddSingleEntry
36: [ OK ] StringTableTest.AddSingleEntry (3 ms)
36: [ RUN ] StringTableTest.CanAccessWithAt
36: [ OK ] StringTableTest.CanAccessWithAt (2 ms)
36: [ RUN ] StringTableTest.CanAccessWithBracket
36: [ OK ] StringTableTest.CanAccessWithBracket (1 ms)
36: [ RUN ] StringTableTest.ThrowsOutOfRange
36: [ OK ] StringTableTest.ThrowsOutOfRange (2 ms)
36: [ RUN ] StringTableTest.StringCompareIsCorrect
36: [ OK ] StringTableTest.StringCompareIsCorrect (1 ms)
36: [ RUN ] StringTableTest.AddTwoDistinctEntries
36: [ OK ] StringTableTest.AddTwoDistinctEntries (2 ms)
36: [ RUN ] StringTableTest.TryToAddDuplicates
36: [ OK ] StringTableTest.TryToAddDuplicates (1 ms)
36: [ RUN ] StringTableTest.AddLargeNumberOfEntries
36: [ OK ] StringTableTest.AddLargeNumberOfEntries (1 ms)
36: [ RUN ] StringTableTest.NoDuplicatesInLargeTable
36: [ OK ] StringTableTest.NoDuplicatesInLargeTable (1 ms)
36: [ RUN ] StringTableTest.CanWriteToBuffer
36: [ OK ] StringTableTest.CanWriteToBuffer (1 ms)
36: [ RUN ] StringTableTest.Roundtrip
36: [ OK ] StringTableTest.Roundtrip (0 ms)
36: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices
36: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms)
36: [ RUN ] StringTableTest.CanCopyToLegacyTable
36: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms)
36: [----------] 13 tests from StringTableTest (15 ms total)
36:
36: [----------] 6 tests from LegacySymtabTest
36: [ RUN ] LegacySymtabTest.EmptyOnOpen
36: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms)
36: [ RUN ] LegacySymtabTest.AddSingleEntry
36: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms)
36: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries
36: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms)
36: [ RUN ] LegacySymtabTest.TryToAddDuplicates
36: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms)
36: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries
36: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms)
36: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable
36: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (1 ms)
36: [----------] 6 tests from LegacySymtabTest (2 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 31 tests from 5 test cases ran. (19 ms total)
36: [ PASSED ] 31 tests.
36/65 Test #36: TopologyTest .......................... Passed 0.10 sec
test 37
Start 37: PullTest
37: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/PullTest.xml"
37: Test timeout computed to be: 30
37: [==========] Running 5 tests from 1 test case.
37: [----------] Global test environment set-up.
37: [----------] 5 tests from PullTest
37: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
37: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
37: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
37: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
37: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
37: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
37: [----------] 5 tests from PullTest (1 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 5 tests from 1 test case ran. (3 ms total)
37: [ PASSED ] 5 tests.
37/65 Test #37: PullTest .............................. Passed 0.07 sec
test 38
Start 38: SimdUnitTests
38: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/SimdUnitTests.xml"
38: Test timeout computed to be: 30
38: [==========] Running 86 tests from 3 test cases.
38: [----------] Global test environment set-up.
38: [----------] 41 tests from SimdScalarTest
38: [ RUN ] SimdScalarTest.load
38: [ OK ] SimdScalarTest.load (0 ms)
38: [ RUN ] SimdScalarTest.loadU
38: [ OK ] SimdScalarTest.loadU (0 ms)
38: [ RUN ] SimdScalarTest.store
38: [ OK ] SimdScalarTest.store (0 ms)
38: [ RUN ] SimdScalarTest.storeU
38: [ OK ] SimdScalarTest.storeU (0 ms)
38: [ RUN ] SimdScalarTest.setZero
38: [ OK ] SimdScalarTest.setZero (0 ms)
38: [ RUN ] SimdScalarTest.andNot
38: [ OK ] SimdScalarTest.andNot (0 ms)
38: [ RUN ] SimdScalarTest.fma
38: [ OK ] SimdScalarTest.fma (0 ms)
38: [ RUN ] SimdScalarTest.fms
38: [ OK ] SimdScalarTest.fms (0 ms)
38: [ RUN ] SimdScalarTest.fnma
38: [ OK ] SimdScalarTest.fnma (0 ms)
38: [ RUN ] SimdScalarTest.fnms
38: [ OK ] SimdScalarTest.fnms (0 ms)
38: [ RUN ] SimdScalarTest.maskAdd
38: [ OK ] SimdScalarTest.maskAdd (0 ms)
38: [ RUN ] SimdScalarTest.maskzMul
38: [ OK ] SimdScalarTest.maskzMul (0 ms)
38: [ RUN ] SimdScalarTest.maskzFma
38: [ OK ] SimdScalarTest.maskzFma (0 ms)
38: [ RUN ] SimdScalarTest.abs
38: [ OK ] SimdScalarTest.abs (0 ms)
38: [ RUN ] SimdScalarTest.max
38: [ OK ] SimdScalarTest.max (0 ms)
38: [ RUN ] SimdScalarTest.min
38: [ OK ] SimdScalarTest.min (1 ms)
38: [ RUN ] SimdScalarTest.round
38: [ OK ] SimdScalarTest.round (0 ms)
38: [ RUN ] SimdScalarTest.trunc
38: [ OK ] SimdScalarTest.trunc (0 ms)
38: [ RUN ] SimdScalarTest.reduce
38: [ OK ] SimdScalarTest.reduce (0 ms)
38: [ RUN ] SimdScalarTest.testBits
38: [ OK ] SimdScalarTest.testBits (0 ms)
38: [ RUN ] SimdScalarTest.anyTrue
38: [ OK ] SimdScalarTest.anyTrue (0 ms)
38: [ RUN ] SimdScalarTest.selectByMask
38: [ OK ] SimdScalarTest.selectByMask (0 ms)
38: [ RUN ] SimdScalarTest.selectByNotMask
38: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
38: [ RUN ] SimdScalarTest.blend
38: [ OK ] SimdScalarTest.blend (0 ms)
38: [ RUN ] SimdScalarTest.cvtR2I
38: [ OK ] SimdScalarTest.cvtR2I (0 ms)
38: [ RUN ] SimdScalarTest.cvttR2I
38: [ OK ] SimdScalarTest.cvttR2I (0 ms)
38: [ RUN ] SimdScalarTest.cvtI2R
38: [ OK ] SimdScalarTest.cvtI2R (0 ms)
38: [ RUN ] SimdScalarTest.cvtF2D
38: [ OK ] SimdScalarTest.cvtF2D (0 ms)
38: [ RUN ] SimdScalarTest.cvtD2D
38: [ OK ] SimdScalarTest.cvtD2D (0 ms)
38: [ RUN ] SimdScalarTest.loadI
38: [ OK ] SimdScalarTest.loadI (0 ms)
38: [ RUN ] SimdScalarTest.loadUI
38: [ OK ] SimdScalarTest.loadUI (0 ms)
38: [ RUN ] SimdScalarTest.storeI
38: [ OK ] SimdScalarTest.storeI (0 ms)
38: [ RUN ] SimdScalarTest.storeUI
38: [ OK ] SimdScalarTest.storeUI (0 ms)
38: [ RUN ] SimdScalarTest.andNotI
38: [ OK ] SimdScalarTest.andNotI (0 ms)
38: [ RUN ] SimdScalarTest.testBitsI
38: [ OK ] SimdScalarTest.testBitsI (0 ms)
38: [ RUN ] SimdScalarTest.selectByMaskI
38: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
38: [ RUN ] SimdScalarTest.selectByNotMaskI
38: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
38: [ RUN ] SimdScalarTest.blendI
38: [ OK ] SimdScalarTest.blendI (0 ms)
38: [ RUN ] SimdScalarTest.cvtB2IB
38: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
38: [ RUN ] SimdScalarTest.cvtIB2B
38: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
38: [ RUN ] SimdScalarTest.expandScalarsToTriplets
38: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
38: [----------] 41 tests from SimdScalarTest (17 ms total)
38:
38: [----------] 8 tests from SimdScalarUtilTest
38: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
38: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
38: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
38: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
38: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
38: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
38: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
38: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
38: [----------] 8 tests from SimdScalarUtilTest (4 ms total)
38:
38: [----------] 37 tests from SimdScalarMathTest
38: [ RUN ] SimdScalarMathTest.copysign
38: [ OK ] SimdScalarMathTest.copysign (0 ms)
38: [ RUN ] SimdScalarMathTest.invsqrtPair
38: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
38: [ RUN ] SimdScalarMathTest.inv
38: [ OK ] SimdScalarMathTest.inv (0 ms)
38: [ RUN ] SimdScalarMathTest.maskzInvsqrt
38: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
38: [ RUN ] SimdScalarMathTest.log
38: [ OK ] SimdScalarMathTest.log (0 ms)
38: [ RUN ] SimdScalarMathTest.exp2
38: [ OK ] SimdScalarMathTest.exp2 (0 ms)
38: [ RUN ] SimdScalarMathTest.exp
38: [ OK ] SimdScalarMathTest.exp (0 ms)
38: [ RUN ] SimdScalarMathTest.erf
38: [ OK ] SimdScalarMathTest.erf (0 ms)
38: [ RUN ] SimdScalarMathTest.erfc
38: [ OK ] SimdScalarMathTest.erfc (0 ms)
38: [ RUN ] SimdScalarMathTest.sincos
38: [ OK ] SimdScalarMathTest.sincos (0 ms)
38: [ RUN ] SimdScalarMathTest.sin
38: [ OK ] SimdScalarMathTest.sin (0 ms)
38: [ RUN ] SimdScalarMathTest.cos
38: [ OK ] SimdScalarMathTest.cos (0 ms)
38: [ RUN ] SimdScalarMathTest.tan
38: [ OK ] SimdScalarMathTest.tan (0 ms)
38: [ RUN ] SimdScalarMathTest.asin
38: [ OK ] SimdScalarMathTest.asin (0 ms)
38: [ RUN ] SimdScalarMathTest.acos
38: [ OK ] SimdScalarMathTest.acos (0 ms)
38: [ RUN ] SimdScalarMathTest.atan
38: [ OK ] SimdScalarMathTest.atan (0 ms)
38: [ RUN ] SimdScalarMathTest.atan2
38: [ OK ] SimdScalarMathTest.atan2 (0 ms)
38: [ RUN ] SimdScalarMathTest.pmeForceCorrection
38: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
38: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
38: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
38: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
38: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.invSingleAccuracy
38: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
38: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.logSingleAccuracy
38: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
38: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.expSingleAccuracy
38: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
38: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
38: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
38: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
38: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
38: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
38: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
38: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
38: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
38: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
38: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
38: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
38: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
38: [----------] 37 tests from SimdScalarMathTest (6 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 86 tests from 3 test cases ran. (28 ms total)
38: [ PASSED ] 86 tests.
38/65 Test #38: SimdUnitTests ......................... Passed 0.10 sec
test 39
Start 39: CompatibilityHelpersTests
39: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml"
39: Test timeout computed to be: 30
39: [==========] Running 9 tests from 6 test cases.
39: [----------] Global test environment set-up.
39: [----------] 4 tests from TemplateMPTest
39: [ RUN ] TemplateMPTest.MpWithIndexInt
39: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms)
39: [ RUN ] TemplateMPTest.MpWithIndexIntBad
39: [ OK ] TemplateMPTest.MpWithIndexIntBad (1 ms)
39: [ RUN ] TemplateMPTest.MpWithIndexBool
39: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms)
39: [ RUN ] TemplateMPTest.MpWithIndexEnum
39: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms)
39: [----------] 4 tests from TemplateMPTest (1 ms total)
39:
39: [----------] 1 test from NotNullConstruction
39: [ RUN ] NotNullConstruction.Works
39: [ OK ] NotNullConstruction.Works (0 ms)
39: [----------] 1 test from NotNullConstruction (0 ms total)
39:
39: [----------] 1 test from NotNullCasting
39: [ RUN ] NotNullCasting.Works
39: [ OK ] NotNullCasting.Works (0 ms)
39: [----------] 1 test from NotNullCasting (0 ms total)
39:
39: [----------] 1 test from NotNullAssignment
39: [ RUN ] NotNullAssignment.Works
39: [ OK ] NotNullAssignment.Works (0 ms)
39: [----------] 1 test from NotNullAssignment (0 ms total)
39:
39: [----------] 1 test from MakeNotNull
39: [ RUN ] MakeNotNull.Works
39: [ OK ] MakeNotNull.Works (0 ms)
39: [----------] 1 test from MakeNotNull (0 ms total)
39:
39: [----------] 1 test from NotNull
39: [ RUN ] NotNull.WorksInContainers
39: [ OK ] NotNull.WorksInContainers (0 ms)
39: [----------] 1 test from NotNull (0 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 9 tests from 6 test cases ran. (1 ms total)
39: [ PASSED ] 9 tests.
39/65 Test #39: CompatibilityHelpersTests ............. Passed 0.07 sec
test 40
Start 40: GmxAnaTest
40: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxAnaTest.xml"
40: Test timeout computed to be: 600
40: [==========] Running 27 tests from 5 test cases.
40: [----------] Global test environment set-up.
40: [----------] 5 tests from Entropy
40: [ RUN ] Entropy.Schlitter_300_NoLinear
40: [ OK ] Entropy.Schlitter_300_NoLinear (2 ms)
40: [ RUN ] Entropy.Schlitter_300_Linear
40: [ OK ] Entropy.Schlitter_300_Linear (0 ms)
40: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
40: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (1 ms)
40: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
40: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (1 ms)
40: [ RUN ] Entropy.QuasiHarmonic_200_Linear
40: [ OK ] Entropy.QuasiHarmonic_200_Linear (1 ms)
40: [----------] 5 tests from Entropy (7 ms total)
40:
40: [----------] 10 tests from MindistTest
40: [ RUN ] MindistTest.mindistWorksWithSingleAtoms
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.mindistWorksWithSingleAtoms (48 ms)
40: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 2: 'atom3'
40: Selected 3: 'atoms12'
40: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (6 ms)
40: [ RUN ] MindistTest.mindistDoesNotPickUpContacts
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.mindistDoesNotPickUpContacts (6 ms)
40: [ RUN ] MindistTest.mindistPicksUpContacts
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.mindistPicksUpContacts (7 ms)
40: [ RUN ] MindistTest.ngWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: Selected 2: 'atom3'
40: [ OK ] MindistTest.ngWorks (6 ms)
40: [ RUN ] MindistTest.groupWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 3: 'atoms12'
40: Selected 2: 'atom3'
40: [ OK ] MindistTest.groupWorks (6 ms)
40: [ RUN ] MindistTest.maxDistWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 2: 'atom3'
40: Selected 3: 'atoms12'
40: [ OK ] MindistTest.maxDistWorks (6 ms)
40: [ RUN ] MindistTest.noPbcWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.noPbcWorks (5 ms)
40: [ RUN ] MindistTest.resPerTimeWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 3: 'atoms12'
40: Selected 2: 'atom3'
40: [ OK ] MindistTest.resPerTimeWorks (6 ms)
40: [ RUN ] MindistTest.matrixWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 5: 'atoms123'
40: Special case: making distance matrix between all atoms in group atoms123
40: [ OK ] MindistTest.matrixWorks (5 ms)
40: [----------] 10 tests from MindistTest (107 ms total)
40:
40: [----------] 3 tests from MsdTest
40: [ RUN ] MsdTest.threeDimensionalDiffusion
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( particles) has 3 elements
40: There is one group in the index
40:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
40:
40: Used 1 restart points spaced 200 ps over 9 ps
40:
40: Fitting from 1 to 8 ps
40:
40: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
40: [ OK ] MsdTest.threeDimensionalDiffusion (8 ms)
40: [ RUN ] MsdTest.twoDimensionalDiffusion
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( particles) has 3 elements
40: There is one group in the index
40:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
40:
40: Used 1 restart points spaced 200 ps over 9 ps
40:
40: Fitting from 1 to 8 ps
40:
40: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
40: [ OK ] MsdTest.twoDimensionalDiffusion (6 ms)
40: [ RUN ] MsdTest.oneDimensionalDiffusion
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( particles) has 3 elements
40: There is one group in the index
40:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
40:
40: Used 1 restart points spaced 200 ps over 9 ps
40:
40: Fitting from 1 to 8 ps
40:
40: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
40: [ OK ] MsdTest.oneDimensionalDiffusion (6 ms)
40: [----------] 3 tests from MsdTest (21 ms total)
40:
40: [----------] 3 tests from MsdMolTest
40: [ RUN ] MsdMolTest.diffMolMassWeighted
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Generating 1-4 interactions: fudge = 0.5
40: Number of degrees of freedom in T-Coupling group rest is 27.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Calculating diffusion coefficients for molecules.
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( water) has 15 elements
40: There is one group in the index
40: Split group of 15 atoms into 5 molecules
40: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
40:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
40:
40: Used 1 restart points spaced 200 ps over 0.1 ps
40:
40: Setting the LD random seed to -17433217
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40:
40: Generated 330891 of the 330891 1-4 parameter combinations
40:
40: Excluding 2 bonded neighbours molecule type 'SOL'
40:
40: This run will generate roughly 0 Mb of data
40: Wrote per-molecule output to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted_msdmol.xvg
40: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
40: Fitting from 0.008 to 0.088 ps
40:
40: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
40: [ OK ] MsdMolTest.diffMolMassWeighted (4350 ms)
40: [ RUN ] MsdMolTest.diffMolNonMassWeighted
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Generating 1-4 interactions: fudge = 0.5
40: Number of degrees of freedom in T-Coupling group rest is 27.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Calculating diffusion coefficients for molecules.
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( water) has 15 elements
40: There is one group in the index
40: Split group of 15 atoms into 5 molecules
40: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
40:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
40:
40: Used 1 restart points spaced 200 ps over 0.1 ps
40:
40: Setting the LD random seed to -9846851
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40:
40: Generated 330891 of the 330891 1-4 parameter combinations
40:
40: Excluding 2 bonded neighbours molecule type 'SOL'
40:
40: This run will generate roughly 0 Mb of data
40: Wrote per-molecule output to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted_msdmol.xvg
40: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
40: Fitting from 0.008 to 0.088 ps
40:
40: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
40: [ OK ] MsdMolTest.diffMolNonMassWeighted (4241 ms)
40: [ RUN ] MsdMolTest.diffMolSelected
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Generating 1-4 interactions: fudge = 0.5
40: Number of degrees of freedom in T-Coupling group rest is 27.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Calculating diffusion coefficients for molecules.
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( mol) has 9 elements
40: There is one group in the index
40: Split group of 9 atoms into 3 molecules
40: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
40:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
40:
40: Used 1 restart points spaced 200 ps over 0.1 ps
40:
40: Setting the LD random seed to -138480131
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40:
40: Generated 330891 of the 330891 1-4 parameter combinations
40:
40: Excluding 2 bonded neighbours molecule type 'SOL'
40:
40: This run will generate roughly 0 Mb of data
40: Wrote per-molecule output to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected_msdmol.xvg
40: <D> = 7.3593 Std. Dev. = 9.7910 Error = 5.6529
40: Fitting from 0.008 to 0.088 ps
40:
40: D[ mol] 7.8614 (+/- 1.5619) 1e-5 cm^2/s
40: [ OK ] MsdMolTest.diffMolSelected (4376 ms)
40: [----------] 3 tests from MsdMolTest (12969 ms total)
40:
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group: trr version: GMX_trn_file (single precision)
40:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (54 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (30 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (48 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group: Reading frames from gro file '', 6 atoms.
40:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (29 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
40:
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (10 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (40 ms)
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (211 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 27 tests from 5 test cases ran. (13315 ms total)
40: [ PASSED ] 27 tests.
40/65 Test #40: GmxAnaTest ............................ Passed 13.42 sec
test 41
Start 41: GmxPreprocessTests
41: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml"
41: Test timeout computed to be: 1920
41: [==========] Running 51 tests from 9 test cases.
41: [----------] Global test environment set-up.
41: [----------] 4 tests from GenconfTest
41: [ RUN ] GenconfTest.nbox_Works
41: [ OK ] GenconfTest.nbox_Works (23 ms)
41: [ RUN ] GenconfTest.nbox_norenumber_Works
41: [ OK ] GenconfTest.nbox_norenumber_Works (34 ms)
41: [ RUN ] GenconfTest.nbox_dist_Works
41: [ OK ] GenconfTest.nbox_dist_Works (40 ms)
41: [ RUN ] GenconfTest.nbox_rot_Works
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: [ OK ] GenconfTest.nbox_rot_Works (19 ms)
41: [----------] 4 tests from GenconfTest (116 ms total)
41:
41: [----------] 2 tests from GenionTest
41: [ RUN ] GenionTest.HighConcentrationIonPlacement
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
41: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
41: buffer. The cluster pair list does have a buffering effect, but choosing
41: a larger rlist might be necessary for good energy conservation.
41:
41:
41: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: Generating 1-4 interactions: fudge = 0.5
41: Number of degrees of freedom in T-Coupling group rest is 1308.00
41:
41: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
41: You are using a plain Coulomb cut-off, which might produce artifacts.
41: You might want to consider using PME electrostatics.
41:
41:
41:
41: There were 3 notes
41: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
41: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
41: Group 0 ( System) has 653 elements
41: Group 1 ( Water) has 648 elements
41: Group 2 ( SOL) has 648 elements
41: Group 3 ( non-Water) has 5 elements
41: Group 4 ( Other) has 5 elements
41: Group 5 ( METH) has 5 elements
41: Select a group: Number of (3-atomic) solvent molecules: 216
41: Using random seed 1997.
41: Replacing solvent molecule 56 (atom 168) with NA
41: Replacing solvent molecule 120 (atom 360) with NA
41: Replacing solvent molecule 182 (atom 546) with NA
41: Replacing solvent molecule 71 (atom 213) with NA
41: Replacing solvent molecule 189 (atom 567) with CL
41: Replacing solvent molecule 54 (atom 162) with CL
41: Replacing solvent molecule 155 (atom 465) with CL
41: Replacing solvent molecule 99 (atom 297) with CL
41:
41: Setting the LD random seed to 468967103
41:
41: Generated 331705 of the 331705 non-bonded parameter combinations
41:
41: Generated 331705 of the 331705 1-4 parameter combinations
41:
41: Excluding 2 bonded neighbours molecule type 'SOL'
41:
41: Excluding 3 bonded neighbours molecule type 'methane'
41: Analysing residue names:
41: There are: 216 Water residues
41: There are: 1 Other residues
41: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
41:
41: This run will generate roughly 0 Mb of data
41: Will try to add 4 NA ions and 4 CL ions.
41: Select a continuous group of solvent molecules
41: Selected 1: 'Water'
41: [ OK ] GenionTest.HighConcentrationIonPlacement (4093 ms)
41: [ RUN ] GenionTest.NoIonPlacement
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
41: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
41: buffer. The cluster pair list does have a buffering effect, but choosing
41: a larger rlist might be necessary for good energy conservation.
41:
41:
41: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: Generating 1-4 interactions: fudge = 0.5
41: Number of degrees of freedom in T-Coupling group rest is 1308.00
41:
41: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
41: You are using a plain Coulomb cut-off, which might produce artifacts.
41: You might want to consider using PME electrostatics.
41:
41:
41:
41: There were 3 notes
41: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
41: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
41: No ions to add, will just copy input configuration.
41: Setting the LD random seed to -676364417
41:
41: Generated 331705 of the 331705 non-bonded parameter combinations
41:
41: Generated 331705 of the 331705 1-4 parameter combinations
41:
41: Excluding 2 bonded neighbours molecule type 'SOL'
41:
41: Excluding 3 bonded neighbours molecule type 'methane'
41: Analysing residue names:
41: There are: 216 Water residues
41: There are: 1 Other residues
41: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
41:
41: This run will generate roughly 0 Mb of data
41: [ OK ] GenionTest.NoIonPlacement (3985 ms)
41: [----------] 2 tests from GenionTest (8083 ms total)
41:
41: [----------] 1 test from GenRestrTest
41: [ RUN ] GenRestrTest.SimpleRestraintsGenerated
41:
41: Reading structure file
41: Group 0 ( System) has 156 elements
41: Group 1 ( Protein) has 156 elements
41: Group 2 ( Protein-H) has 75 elements
41: Group 3 ( C-alpha) has 10 elements
41: Group 4 ( Backbone) has 30 elements
41: Group 5 ( MainChain) has 40 elements
41: Group 6 ( MainChain+Cb) has 49 elements
41: Group 7 ( MainChain+H) has 52 elements
41: Group 8 ( SideChain) has 104 elements
41: Group 9 ( SideChain-H) has 35 elements
41: Select a group: Select group to position restrain
41: Selected 3: 'C-alpha'
41: [ OK ] GenRestrTest.SimpleRestraintsGenerated (15 ms)
41: [----------] 1 test from GenRestrTest (16 ms total)
41:
41: [----------] 9 tests from PreprocessingAtomTypesTest
41: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate
41: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid
41: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks
41: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks
41: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry
41: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound
41: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound
41: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber
41: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber
41: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms)
41: [----------] 9 tests from PreprocessingAtomTypesTest (2 ms total)
41:
41: [----------] 10 tests from PreprocessingBondAtomTypeTest
41: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate
41: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid
41: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks
41: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks
41: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry
41: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType
41: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound
41: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound
41: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber
41: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber
41: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms)
41: [----------] 10 tests from PreprocessingBondAtomTypeTest (2 ms total)
41:
41: [----------] 5 tests from InsertMoleculesTest
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
41: Reading solute configuration
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 8 atoms)!
41:
41: Added 1 molecules (out of 1 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
41:
41: Output configuration contains 8 atoms in 4 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (50 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 2 atoms)!
41:
Try 2 success (now 4 atoms)!
41:
Try 3 success (now 6 atoms)!
41:
Try 4 success (now 8 atoms)!
41:
Try 5 success (now 10 atoms)!
41:
41: Added 5 molecules (out of 5 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
41:
41: Output configuration contains 10 atoms in 10 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (19 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
41: Reading solute configuration
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 8 atoms)!
41:
Try 2 success (now 10 atoms)!
41:
41: Added 2 molecules (out of 2 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
41:
41: Output configuration contains 10 atoms in 4 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (11 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
41: Reading solute configuration
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 650 atoms)!
41:
Try 2 success (now 652 atoms)!
41:
Try 3 success (now 654 atoms)!
41:
Try 4 success (now 656 atoms)!
41:
41: Added 4 molecules (out of 4 requested)
41: Replaced 8 residues (24 atoms)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
41:
41: Output configuration contains 632 atoms in 212 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (69 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
41:
41:
Try 1 success (now 2 atoms)!
41:
Try 2 success (now 4 atoms)!
41:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
41:
Try 13 success (now 6 atoms)!
41:
41: Added 3 molecules (out of 4 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
41:
41: Output configuration contains 6 atoms in 3 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (10 ms)
41: [----------] 5 tests from InsertMoleculesTest (160 ms total)
41:
41: [----------] 14 tests from GetIrTest
41: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
41: Ignoring obsolete mdp entry 'title'
41: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (35 ms)
41: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals
41: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (29 ms)
41: [ RUN ] GetIrTest.AcceptsKeyWithoutValue
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsKeyWithoutValue (20 ms)
41: [ RUN ] GetIrTest.RejectsValueWithoutKey
41: [ OK ] GetIrTest.RejectsValueWithoutKey (29 ms)
41: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue
41: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (28 ms)
41: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (28 ms)
41: [ RUN ] GetIrTest.AcceptsEmptyLines
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsEmptyLines (23 ms)
41: [ RUN ] GetIrTest.AcceptsElectricField
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsElectricField (18 ms)
41: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (17 ms)
41: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (18 ms)
41: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys
41: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (12 ms)
41: [ RUN ] GetIrTest.AcceptsImplicitSolventNo
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsImplicitSolventNo (18 ms)
41: [ RUN ] GetIrTest.RejectsImplicitSolventYes
41: [ OK ] GetIrTest.RejectsImplicitSolventYes (28 ms)
41: [ RUN ] GetIrTest.AcceptsMimic
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsMimic (20 ms)
41: [----------] 14 tests from GetIrTest (324 ms total)
41:
41: [----------] 5 tests from SolvateTest
41: [ RUN ] SolvateTest.cs_box_Works
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 1x1x1 boxes
41: Solvent box contains 270 atoms in 90 residues
41: Removed 129 solvent atoms due to solvent-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 47 residues
41: Generated solvent containing 141 atoms in 47 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
41:
41: Output configuration contains 141 atoms in 47 residues
41: Volume : 1.331 (nm^3)
41: Density : 1056.36 (g/l)
41: Number of solvent molecules: 47
41:
41: [ OK ] SolvateTest.cs_box_Works (98 ms)
41: [ RUN ] SolvateTest.cs_cp_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 2x2x2 boxes
41: Solvent box contains 3660 atoms in 1220 residues
41: Removed 987 solvent atoms due to solvent-solvent overlap
41: Removed 15 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 886 residues
41: Generated solvent containing 2658 atoms in 886 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
41:
41: Output configuration contains 2664 atoms in 888 residues
41: Volume : 27.2709 (nm^3)
41: Density : 974.777 (g/l)
41: Number of solvent molecules: 886
41:
41: [ OK ] SolvateTest.cs_cp_Works (309 ms)
41: [ RUN ] SolvateTest.cs_cp_p_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 2x2x2 boxes
41: Solvent box contains 3660 atoms in 1220 residues
41: Removed 987 solvent atoms due to solvent-solvent overlap
41: Removed 15 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 886 residues
41: Generated solvent containing 2658 atoms in 886 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
41:
41: Output configuration contains 2664 atoms in 888 residues
41: Volume : 27.2709 (nm^3)
41: Density : 974.777 (g/l)
41: Number of solvent molecules: 886
41:
41: Processing topology
41: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top)
41: [ OK ] SolvateTest.cs_cp_p_Works (397 ms)
41: [ RUN ] SolvateTest.shell_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 2x2x2 boxes
41: Solvent box contains 3660 atoms in 1220 residues
41: Removed 987 solvent atoms due to solvent-solvent overlap
41: Removed 1902 solvent atoms more than 1.000000 nm from solute.
41: Removed 15 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 252 residues
41: Generated solvent containing 756 atoms in 252 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
41:
41: Output configuration contains 762 atoms in 254 residues
41: Volume : 27.2709 (nm^3)
41: Density : 279.3 (g/l)
41: Number of solvent molecules: 252
41:
41: [ OK ] SolvateTest.shell_Works (169 ms)
41: [ RUN ] SolvateTest.update_Topology_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 3x3x3 boxes
41: Solvent box contains 14952 atoms in 4984 residues
41: Removed 2787 solvent atoms due to solvent-solvent overlap
41: Removed 30 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 2 different molecule types:
41: HOH ( 3 atoms): 1876 residues
41: SOL ( 3 atoms): 2169 residues
41: Generated solvent containing 0 atoms in 0 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
41:
41: Output configuration contains 12141 atoms in 4047 residues
41: Volume : 125 (nm^3)
41: Density : 968.963 (g/l)
41: Number of solvent molecules: 4045
41:
41: Processing topology
41: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
41: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
41: [ OK ] SolvateTest.update_Topology_Works (1408 ms)
41: [----------] 5 tests from SolvateTest (2382 ms total)
41:
41: [----------] 1 test from TopDirTests
41: [ RUN ] TopDirTests.NamesArrayHasCorrectSize
41: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms)
41: [----------] 1 test from TopDirTests (0 ms total)
41:
41: [----------] Global test environment tear-down
41: [==========] 51 tests from 9 test cases ran. (11089 ms total)
41: [ PASSED ] 51 tests.
41/65 Test #41: GmxPreprocessTests .................... Passed 11.16 sec
test 42
Start 42: Pdb2gmx1Test
42: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml"
42: Test timeout computed to be: 1920
42: [==========] Running 24 tests from 1 test case.
42: [----------] Global test environment set-up.
42: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 0 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (782 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 0 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (779 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 0 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (822 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 0 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (559 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Marked 124 virtual sites
42: Added 16 dummy masses
42: Added 26 new constraints
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 130 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (678 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Marked 132 virtual sites
42: Added 10 dummy masses
42: Added 19 new constraints
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 133 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (695 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Marked 123 virtual sites
42: Added 22 dummy masses
42: Added 35 new constraints
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 132 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (648 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Marked 111 virtual sites
42: Added 18 dummy masses
42: Added 31 new constraints
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 116 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (595 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 0 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (592 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 0 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (666 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 0 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (593 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 0 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (555 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Marked 124 virtual sites
42: Added 16 dummy masses
42: Added 26 new constraints
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 130 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (622 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Marked 132 virtual sites
42: Added 10 dummy masses
42: Added 19 new constraints
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 133 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (692 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Marked 123 virtual sites
42: Added 22 dummy masses
42: Added 35 new constraints
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 132 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (647 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Marked 111 virtual sites
42: Added 18 dummy masses
42: Added 31 new constraints
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 116 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (595 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 0 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (580 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 0 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (652 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 0 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (600 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 0 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (539 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Marked 124 virtual sites
42: Added 16 dummy masses
42: Added 26 new constraints
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 130 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (632 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Marked 132 virtual sites
42: Added 10 dummy masses
42: Added 19 new constraints
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 133 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (688 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Marked 123 virtual sites
42: Added 22 dummy masses
42: Added 35 new constraints
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 132 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (667 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Marked 111 virtual sites
42: Added 18 dummy masses
42: Added 31 new constraints
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 116 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (588 ms)
42: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (15476 ms total)
42:
42: [----------] Global test environment tear-down
42: [==========] 24 tests from 1 test case ran. (15477 ms total)
42: [ PASSED ] 24 tests.
42/65 Test #42: Pdb2gmx1Test .......................... Passed 15.58 sec
test 43
Start 43: Pdb2gmx2Test
43: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml"
43: Test timeout computed to be: 1920
43: [==========] Running 32 tests from 2 test cases.
43: [----------] Global test environment set-up.
43: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (403 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (405 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (376 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (389 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 37 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 37 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (402 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 53 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 51 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (501 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 36 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 36 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (421 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 33 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 31 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (414 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (405 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (451 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (381 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (400 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 37 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 37 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (419 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 53 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 51 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (562 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 36 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 36 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (397 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 33 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 31 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (399 ms)
43: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (6767 ms total)
43:
43: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (613 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (494 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (416 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (553 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 39 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 39 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (437 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 57 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 55 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (631 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 38 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 38 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (454 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 35 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 33 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (392 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (401 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (490 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (421 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (389 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 39 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 39 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (405 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 57 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 55 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (494 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 38 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 38 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (464 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 35 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 33 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (414 ms)
43: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (7498 ms total)
43:
43: [----------] Global test environment tear-down
43: [==========] 32 tests from 2 test cases ran. (14266 ms total)
43: [ PASSED ] 32 tests.
43/65 Test #43: Pdb2gmx2Test .......................... Passed 14.36 sec
test 44
Start 44: Pdb2gmx3Test
44: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml"
44: Test timeout computed to be: 1920
44: [==========] Running 33 tests from 6 test cases.
44: [----------] Global test environment set-up.
44: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 653 pairs
44: Before cleaning: 691 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 255, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 691 dihedrals, 51 impropers, 457 angles
44: 650 pairs, 254 bonds and 0 virtual sites
44:
44: Total mass 1846.132 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (659 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 748 pairs
44: Before cleaning: 788 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 291, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 788 dihedrals, 72 impropers, 516 angles
44: 736 pairs, 290 bonds and 0 virtual sites
44:
44: Total mass 2088.366 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (626 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 676 pairs
44: Before cleaning: 727 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 262, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 727 dihedrals, 56 impropers, 472 angles
44: 667 pairs, 261 bonds and 0 virtual sites
44:
44: Total mass 1861.124 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (524 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 603 pairs
44: Before cleaning: 634 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 233, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 634 dihedrals, 48 impropers, 419 angles
44: 597 pairs, 232 bonds and 0 virtual sites
44:
44: Total mass 1662.888 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (546 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 124 virtual sites
44: Added 16 dummy masses
44: Added 26 new constraints
44: Before cleaning: 653 pairs
44: Before cleaning: 691 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 255, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 691 dihedrals, 51 impropers, 457 angles
44: 650 pairs, 254 bonds and 130 virtual sites
44:
44: Total mass 1846.132 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (750 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 132 virtual sites
44: Added 10 dummy masses
44: Added 19 new constraints
44: Before cleaning: 748 pairs
44: Before cleaning: 788 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 291, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 788 dihedrals, 72 impropers, 516 angles
44: 736 pairs, 290 bonds and 133 virtual sites
44:
44: Total mass 2088.366 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (724 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 123 virtual sites
44: Added 22 dummy masses
44: Added 35 new constraints
44: Before cleaning: 676 pairs
44: Before cleaning: 727 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 262, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 727 dihedrals, 56 impropers, 472 angles
44: 667 pairs, 261 bonds and 132 virtual sites
44:
44: Total mass 1861.124 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (627 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 111 virtual sites
44: Added 18 dummy masses
44: Added 31 new constraints
44: Before cleaning: 603 pairs
44: Before cleaning: 634 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 233, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 634 dihedrals, 48 impropers, 419 angles
44: 597 pairs, 232 bonds and 116 virtual sites
44:
44: Total mass 1662.888 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (558 ms)
44: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (5020 ms total)
44:
44: [----------] 1 test from ForAmber99sb_ildnWithTip4p/Pdb2gmxTest
44: [ RUN ] ForAmber99sb_ildnWithTip4p/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/tip4p.pdb...
44: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 2 4 (only water)
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (4 atoms, 2 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 2 residues with 8 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 4, now 4
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 2 angles
44: 0 pairs, 4 bonds and 0 virtual sites
44:
44: Total mass 36.032 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/tip4p.pdb.
44:
44: The Amber99sb-ildn force field and the tip4p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildnWithTip4p/Pdb2gmxTest.ProducesMatchingTopology/0 (264 ms)
44: [----------] 1 test from ForAmber99sb_ildnWithTip4p/Pdb2gmxTest (267 ms total)
44:
44: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 653 pairs
44: Before cleaning: 663 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 254, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 663 dihedrals, 48 impropers, 457 angles
44: 650 pairs, 254 bonds and 0 virtual sites
44:
44: Total mass 1846.115 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (569 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 748 pairs
44: Before cleaning: 778 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus PHE-33: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 290, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 778 dihedrals, 49 impropers, 516 angles
44: 736 pairs, 290 bonds and 0 virtual sites
44:
44: Total mass 2088.361 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (626 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 676 pairs
44: Before cleaning: 696 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44: Start terminus ALA-34: NH3+
44: End terminus ALA-49: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 261, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 696 dihedrals, 39 impropers, 472 angles
44: 667 pairs, 261 bonds and 0 virtual sites
44:
44: Total mass 1861.130 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (538 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 603 pairs
44: Before cleaning: 618 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44: Start terminus LYS-50: NH3+
44: End terminus PRO-65: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 232, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 618 dihedrals, 38 impropers, 419 angles
44: 597 pairs, 232 bonds and 0 virtual sites
44:
44: Total mass 1662.885 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (437 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 124 virtual sites
44: Added 16 dummy masses
44: Added 26 new constraints
44: Before cleaning: 653 pairs
44: Before cleaning: 663 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 254, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 663 dihedrals, 48 impropers, 457 angles
44: 650 pairs, 254 bonds and 130 virtual sites
44:
44: Total mass 1846.115 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (634 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 132 virtual sites
44: Added 10 dummy masses
44: Added 19 new constraints
44: Before cleaning: 748 pairs
44: Before cleaning: 778 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus PHE-33: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 290, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 778 dihedrals, 49 impropers, 516 angles
44: 736 pairs, 290 bonds and 133 virtual sites
44:
44: Total mass 2088.361 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (594 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 123 virtual sites
44: Added 22 dummy masses
44: Added 35 new constraints
44: Before cleaning: 676 pairs
44: Before cleaning: 696 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44: Start terminus ALA-34: NH3+
44: End terminus ALA-49: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 261, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 696 dihedrals, 39 impropers, 472 angles
44: 667 pairs, 261 bonds and 132 virtual sites
44:
44: Total mass 1861.130 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (617 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 111 virtual sites
44: Added 18 dummy masses
44: Added 31 new constraints
44: Before cleaning: 603 pairs
44: Before cleaning: 618 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44: Start terminus LYS-50: NH3+
44: End terminus PRO-65: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 232, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 618 dihedrals, 38 impropers, 419 angles
44: 597 pairs, 232 bonds and 116 virtual sites
44:
44: Total mass 1662.885 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (500 ms)
44: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (4524 ms total)
44:
44: [----------] 8 tests from ChainSep/Pdb2gmxTest
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 651 pairs
44: Before cleaning: 661 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on changing chain id only (ignoring TER records).
44:
44: Merged chains into joint molecule definitions at 2 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44: Start terminus PHE-6: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 258 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 258, now 258
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 10 cmap torsion pairs
44:
44: There are 661 dihedrals, 46 impropers, 463 angles
44: 648 pairs, 258 bonds and 0 virtual sites
44:
44: Total mass 1882.146 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (504 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 123 pairs
44: Before cleaning: 123 dihedrals
44: Keeping all generated dihedrals
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 10 donors and 7 acceptors were found.
44: There are 7 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS8
44: NE223
44: MET12 SD55 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 317 pairs
44: Before cleaning: 322 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on changing chain id only (ignoring TER records).
44:
44: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 4 28
44:
44: 2 'B' 7 58
44:
44: 3 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (28 atoms, 4 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 4 residues with 51 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 50, now 50
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 2 cmap torsion pairs
44:
44: There are 123 dihedrals, 9 impropers, 88 angles
44: 123 pairs, 50 bonds and 0 virtual sites
44:
44: Total mass 434.421 a.m.u.
44:
44: Total charge -2.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (58 atoms, 7 residues)
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus PHE-6: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 7 residues with 124 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 125, now 125
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 5 cmap torsion pairs
44:
44: There are 322 dihedrals, 19 impropers, 227 angles
44: 314 pairs, 125 bonds and 0 virtual sites
44:
44: Total mass 846.083 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 51 atoms 4 residues
44:
44: Including chain 2 in system: 124 atoms 7 residues
44:
44: Including chain 3 in system: 83 atoms 5 residues
44:
44: Now there are 258 atoms and 16 residues
44:
44: Total mass in system 1882.146 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (377 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 651 pairs
44: Before cleaning: 661 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records only (ignoring chain id).
44:
44: Merged chains into joint molecule definitions at 2 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ILE-9: COO-
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 258 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 258, now 258
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 10 cmap torsion pairs
44:
44: There are 661 dihedrals, 46 impropers, 463 angles
44: 648 pairs, 258 bonds and 0 virtual sites
44:
44: Total mass 1882.146 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (496 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 10 donors and 12 acceptors were found.
44: There are 13 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3
44: SG9
44: HIS8 NE251 1.055
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 288 pairs
44: Before cleaning: 293 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 152 pairs
44: Before cleaning: 152 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records only (ignoring chain id).
44:
44: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 8 61
44:
44: 2 'B' 3 25
44:
44: 3 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (61 atoms, 8 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ILE-9: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 8 residues with 114 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 115, now 115
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 6 cmap torsion pairs
44:
44: There are 293 dihedrals, 23 impropers, 203 angles
44: 285 pairs, 115 bonds and 0 virtual sites
44:
44: Total mass 888.952 a.m.u.
44:
44: Total charge -2.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (25 atoms, 3 residues)
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 61 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 60, now 60
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 152 dihedrals, 5 impropers, 112 angles
44: 152 pairs, 60 bonds and 0 virtual sites
44:
44: Total mass 391.552 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 114 atoms 8 residues
44:
44: Including chain 2 in system: 61 atoms 3 residues
44:
44: Including chain 3 in system: 83 atoms 5 residues
44:
44: Now there are 258 atoms and 16 residues
44:
44: Total mass in system 1882.146 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (319 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 650 pairs
44: Before cleaning: 660 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Merged chains into joint molecule definitions at 3 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44: Start terminus PHE-6: NH3+
44: End terminus ILE-9: COO-
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 261 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 260, now 260
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 8 cmap torsion pairs
44:
44: There are 660 dihedrals, 45 impropers, 466 angles
44: 647 pairs, 260 bonds and 0 virtual sites
44:
44: Total mass 1900.162 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (500 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 123 pairs
44: Before cleaning: 123 dihedrals
44: Keeping all generated dihedrals
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 6 donors and 4 acceptors were found.
44: There are 3 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 164 pairs
44: Before cleaning: 169 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 152 pairs
44: Before cleaning: 152 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 4 28
44:
44: 2 'B' 4 33
44:
44: 3 'B' 3 25
44:
44: 4 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (28 atoms, 4 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 4 residues with 51 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 50, now 50
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 2 cmap torsion pairs
44:
44: There are 123 dihedrals, 9 impropers, 88 angles
44: 123 pairs, 50 bonds and 0 virtual sites
44:
44: Total mass 434.421 a.m.u.
44:
44: Total charge -2.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (33 atoms, 4 residues)
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44: Start terminus PHE-6: NH3+
44: End terminus ILE-9: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 4 residues with 66 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 67, now 67
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 2 cmap torsion pairs
44:
44: There are 169 dihedrals, 13 impropers, 118 angles
44: 161 pairs, 67 bonds and 0 virtual sites
44:
44: Total mass 472.547 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'B' (25 atoms, 3 residues)
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 61 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 60, now 60
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 152 dihedrals, 5 impropers, 112 angles
44: 152 pairs, 60 bonds and 0 virtual sites
44:
44: Total mass 391.552 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Processing chain 4 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 51 atoms 4 residues
44:
44: Including chain 2 in system: 66 atoms 4 residues
44:
44: Including chain 3 in system: 61 atoms 3 residues
44:
44: Including chain 4 in system: 83 atoms 5 residues
44:
44: Now there are 261 atoms and 16 residues
44:
44: Total mass in system 1900.162 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (313 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 652 pairs
44: Before cleaning: 662 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records and chain id changing.
44:
44: Merged chains into joint molecule definitions at 1 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 256, now 256
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 12 cmap torsion pairs
44:
44: There are 662 dihedrals, 47 impropers, 460 angles
44: 649 pairs, 256 bonds and 0 virtual sites
44:
44: Total mass 1864.131 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (521 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 14 donors and 15 acceptors were found.
44: There are 20 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 441 pairs
44: Before cleaning: 446 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records and chain id changing.
44:
44: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 11 86
44:
44: 2 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (86 atoms, 11 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 11 residues with 172 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 173, now 173
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 9 cmap torsion pairs
44:
44: There are 446 dihedrals, 29 impropers, 312 angles
44: 438 pairs, 173 bonds and 0 virtual sites
44:
44: Total mass 1262.488 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 172 atoms 11 residues
44:
44: Including chain 2 in system: 83 atoms 5 residues
44:
44: Now there are 255 atoms and 16 residues
44:
44: Total mass in system 1864.131 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (346 ms)
44: [----------] 8 tests from ChainSep/Pdb2gmxTest (3376 ms total)
44:
44: [----------] 4 tests from ChainChanges/Pdb2gmxTest
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on changing chain id only (ignoring TER records).
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (234 ms)
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records only (ignoring chain id).
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (239 ms)
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (214 ms)
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records and chain id changing.
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (213 ms)
44: [----------] 4 tests from ChainChanges/Pdb2gmxTest (900 ms total)
44:
44: [----------] 4 tests from ForCharmm27CyclicSystem/Pdb2gmxTest
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: WARNING: all CONECT records are ignored
44: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 6040 pairs
44: Before cleaning: 6605 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 6040 pairs
44: Before cleaning: 6605 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb...
44: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: Moved all the water blocks to the end
44:
44: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms
44:
44: chain #res #atoms
44:
44: 1 'P' 71 1527
44:
44: 2 'Q' 71 1527
44:
44: 3 'Q' 7 7
44:
44: 4 ' ' 10 10 (only water)
44:
44: 5 ' ' 16 16 (only water)
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'P' (1527 atoms, 71 residues)
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 71 residues with 2297 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 2481, now 2481
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 6605 dihedrals, 183 impropers, 4434 angles
44: 5827 pairs, 2481 bonds and 0 virtual sites
44:
44: Total mass 22984.514 a.m.u.
44:
44: Total charge -71.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'Q' (1527 atoms, 71 residues)
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 71 residues with 2297 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 2481, now 2481
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 6605 dihedrals, 183 impropers, 4434 angles
44: 5827 pairs, 2481 bonds and 0 virtual sites
44:
44: Total mass 22984.514 a.m.u.
44:
44: Total charge -71.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'Q' (7 atoms, 7 residues)
44:
44: Residue MG72 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG73 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG74 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG75 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG76 has type 'Ion', assuming it is not linked into a chain.
44:
44: Disabling further notes about ions.
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 7 residues with 7 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: No bonds
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 0 angles
44: 0 pairs, 0 bonds and 0 virtual sites
44:
44: Total mass 170.135 a.m.u.
44:
44: Total charge 14.000 e
44:
44: Writing topology
44:
44: Processing chain 4 (10 atoms, 10 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 10 residues with 30 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 30, now 30
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 30 angles
44: 0 pairs, 30 bonds and 0 virtual sites
44:
44: Total mass 180.154 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Processing chain 5 (16 atoms, 16 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 48 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 48, now 48
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 48 angles
44: 0 pairs, 48 bonds and 0 virtual sites
44:
44: Total mass 288.246 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Including chain 1 in system: 2297 atoms 71 residues
44:
44: Including chain 2 in system: 2297 atoms 71 residues
44:
44: Including chain 3 in system: 7 atoms 7 residues
44:
44: Including chain 4 in system: 30 atoms 10 residues
44:
44: Including chain 5 in system: 48 atoms 16 residues
44:
44: Now there are 4679 atoms and 175 residues
44:
44: Total mass in system 46607.563 a.m.u.
44:
44: Total charge in system -128.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/0 (46557 ms)
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 2325 pairs
44: Before cleaning: 2325 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb...
44: Read 'CARNOCYCLIN-A', 413 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 60 413
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (413 atoms, 60 residues)
44:
44: Identified residue LEU1 as a starting terminus.
44:
44: Identified residue LEU60 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 60 residues with 878 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 880, now 880
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 59 cmap torsion pairs
44:
44: There are 2325 dihedrals, 137 impropers, 1614 angles
44: 2319 pairs, 880 bonds and 0 virtual sites
44:
44: Total mass 5866.087 a.m.u.
44:
44: Total charge 4.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/1 (3659 ms)
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: WARNING: all CONECT records are ignored
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 12080 pairs
44: Before cleaning: 13210 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb...
44: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Moved all the water blocks to the end
44:
44: Merged chains into joint molecule definitions at 2 places.
44:
44: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms
44:
44: chain #res #atoms
44:
44: 1 'P' 149 3061
44:
44: 2 ' ' 10 10 (only water)
44:
44: 3 ' ' 16 16 (only water)
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'P' (3061 atoms, 149 residues)
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Residue MG72 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG73 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG74 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG75 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG76 has type 'Ion', assuming it is not linked into a chain.
44:
44: Disabling further notes about ions.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 149 residues with 4601 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 4962, now 4962
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 13210 dihedrals, 366 impropers, 8868 angles
44: 11654 pairs, 4962 bonds and 0 virtual sites
44:
44: Total mass 46139.162 a.m.u.
44:
44: Total charge -128.000 e
44:
44: Writing topology
44:
44: Processing chain 2 (10 atoms, 10 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 10 residues with 30 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 30, now 30
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 30 angles
44: 0 pairs, 30 bonds and 0 virtual sites
44:
44: Total mass 180.154 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Processing chain 3 (16 atoms, 16 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 48 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 48, now 48
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 48 angles
44: 0 pairs, 48 bonds and 0 virtual sites
44:
44: Total mass 288.246 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Including chain 1 in system: 4601 atoms 149 residues
44:
44: Including chain 2 in system: 30 atoms 10 residues
44:
44: Including chain 3 in system: 48 atoms 16 residues
44:
44: Now there are 4679 atoms and 175 residues
44:
44: Total mass in system 46607.563 a.m.u.
44:
44: Total charge in system -128.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/2 (105585 ms)
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 2325 pairs
44: Before cleaning: 2325 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb...
44: Read 'CARNOCYCLIN-A', 413 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 60 413
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (413 atoms, 60 residues)
44:
44: Identified residue LEU1 as a starting terminus.
44:
44: Identified residue LEU60 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 60 residues with 878 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 880, now 880
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 59 cmap torsion pairs
44:
44: There are 2325 dihedrals, 137 impropers, 1614 angles
44: 2319 pairs, 880 bonds and 0 virtual sites
44:
44: Total mass 5866.087 a.m.u.
44:
44: Total charge 4.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/3 (3601 ms)
44: [----------] 4 tests from ForCharmm27CyclicSystem/Pdb2gmxTest (159413 ms total)
44:
44: [----------] Global test environment tear-down
44: [==========] 33 tests from 6 test cases ran. (173502 ms total)
44: [ PASSED ] 33 tests.
44/65 Test #44: Pdb2gmx3Test .......................... Passed 173.59 sec
test 45
Start 45: CorrelationsTest
45: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CorrelationsTest.xml"
45: Test timeout computed to be: 30
45: [==========] Running 21 tests from 3 test cases.
45: [----------] Global test environment set-up.
45: [----------] 10 tests from AutocorrTest
45: [ RUN ] AutocorrTest.EacNormal
45: [ OK ] AutocorrTest.EacNormal (34 ms)
45: [ RUN ] AutocorrTest.EacNoNormalize
45: [ OK ] AutocorrTest.EacNoNormalize (11 ms)
45: [ RUN ] AutocorrTest.EacCos
45: [ OK ] AutocorrTest.EacCos (19 ms)
45: [ RUN ] AutocorrTest.EacVector
45: [ OK ] AutocorrTest.EacVector (46 ms)
45: [ RUN ] AutocorrTest.EacRcross
45: [ OK ] AutocorrTest.EacRcross (9 ms)
45: [ RUN ] AutocorrTest.EacP0
45: [ OK ] AutocorrTest.EacP0 (24 ms)
45: [ RUN ] AutocorrTest.EacP1
45: [ OK ] AutocorrTest.EacP1 (46 ms)
45: [ RUN ] AutocorrTest.EacP2
45: [ OK ] AutocorrTest.EacP2 (51 ms)
45: [ RUN ] AutocorrTest.EacP3
45: [ OK ] AutocorrTest.EacP3 (22 ms)
45: [ RUN ] AutocorrTest.EacP4
45: [ OK ] AutocorrTest.EacP4 (33 ms)
45: [----------] 10 tests from AutocorrTest (304 ms total)
45:
45: [----------] 10 tests from ExpfitTest
45: [ RUN ] ExpfitTest.EffnEXP1
45: [ OK ] ExpfitTest.EffnEXP1 (5 ms)
45: [ RUN ] ExpfitTest.EffnEXP2
45: [ OK ] ExpfitTest.EffnEXP2 (8 ms)
45: [ RUN ] ExpfitTest.EffnEXPEXP
45: [ OK ] ExpfitTest.EffnEXPEXP (12 ms)
45: [ RUN ] ExpfitTest.EffnEXP5
45: [ OK ] ExpfitTest.EffnEXP5 (34 ms)
45: [ RUN ] ExpfitTest.EffnEXP7
45: [ OK ] ExpfitTest.EffnEXP7 (34 ms)
45: [ RUN ] ExpfitTest.EffnEXP9
45: [ OK ] ExpfitTest.EffnEXP9 (130 ms)
45: [ RUN ] ExpfitTest.EffnERF
45: [ OK ] ExpfitTest.EffnERF (19 ms)
45: [ RUN ] ExpfitTest.EffnERREST
45: [ OK ] ExpfitTest.EffnERREST (20 ms)
45: [ RUN ] ExpfitTest.EffnVAC
45: [ OK ] ExpfitTest.EffnVAC (43 ms)
45: [ RUN ] ExpfitTest.EffnPRES
45: [ OK ] ExpfitTest.EffnPRES (99 ms)
45: [----------] 10 tests from ExpfitTest (404 ms total)
45:
45: [----------] 1 test from ManyAutocorrelationTest
45: [ RUN ] ManyAutocorrelationTest.Empty
45: [ OK ] ManyAutocorrelationTest.Empty (1 ms)
45: [----------] 1 test from ManyAutocorrelationTest (1 ms total)
45:
45: [----------] Global test environment tear-down
45: [==========] 21 tests from 3 test cases ran. (763 ms total)
45: [ PASSED ] 21 tests.
45/65 Test #45: CorrelationsTest ...................... Passed 0.83 sec
test 46
Start 46: AnalysisDataUnitTests
46: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml"
46: Test timeout computed to be: 30
46: [==========] Running 69 tests from 14 test cases.
46: [----------] Global test environment set-up.
46: [----------] 3 tests from AnalysisDataInitializationTest
46: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
46: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms)
46: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
46: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (2 ms)
46: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
46: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms)
46: [----------] 3 tests from AnalysisDataInitializationTest (2 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
46: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (14 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (2 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (7 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (4 ms)
46: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (1 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (2 ms)
46: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (1 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/0 (35 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
46: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (5 ms)
46: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (1 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (1 ms)
46: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (2 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/1 (23 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
46: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
46: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (2 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (2 ms)
46: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (2 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/2 (27 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
46: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (4 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (3 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (5 ms)
46: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (2 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (2 ms)
46: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (2 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/3 (27 ms total)
46:
46: [----------] 4 tests from AnalysisArrayDataTest
46: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
46: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (3 ms)
46: [ RUN ] AnalysisArrayDataTest.StorageWorks
46: [ OK ] AnalysisArrayDataTest.StorageWorks (2 ms)
46: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
46: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms)
46: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
46: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
46: [----------] 4 tests from AnalysisArrayDataTest (5 ms total)
46:
46: [----------] 6 tests from AverageModuleTest
46: [ RUN ] AverageModuleTest.BasicTest
46: [ OK ] AverageModuleTest.BasicTest (17 ms)
46: [ RUN ] AverageModuleTest.HandlesMultipointData
46: [ OK ] AverageModuleTest.HandlesMultipointData (9 ms)
46: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
46: [ OK ] AverageModuleTest.HandlesMultipleDataSets (7 ms)
46: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
46: [ OK ] AverageModuleTest.HandlesDataSetAveraging (6 ms)
46: [ RUN ] AverageModuleTest.CanCustomizeXAxis
46: [ OK ] AverageModuleTest.CanCustomizeXAxis (5 ms)
46: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
46: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (4 ms)
46: [----------] 6 tests from AverageModuleTest (49 ms total)
46:
46: [----------] 2 tests from FrameAverageModuleTest
46: [ RUN ] FrameAverageModuleTest.BasicTest
46: [ OK ] FrameAverageModuleTest.BasicTest (4 ms)
46: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
46: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (6 ms)
46: [----------] 2 tests from FrameAverageModuleTest (11 ms total)
46:
46: [----------] 7 tests from AnalysisHistogramSettingsTest
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
46: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total)
46:
46: [----------] 2 tests from SimpleHistogramModuleTest
46: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
46: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (8 ms)
46: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
46: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (7 ms)
46: [----------] 2 tests from SimpleHistogramModuleTest (16 ms total)
46:
46: [----------] 3 tests from WeightedHistogramModuleTest
46: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
46: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (7 ms)
46: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
46: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (7 ms)
46: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
46: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (8 ms)
46: [----------] 3 tests from WeightedHistogramModuleTest (24 ms total)
46:
46: [----------] 3 tests from BinAverageModuleTest
46: [ RUN ] BinAverageModuleTest.ComputesCorrectly
46: [ OK ] BinAverageModuleTest.ComputesCorrectly (6 ms)
46: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
46: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (6 ms)
46: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
46: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (6 ms)
46: [----------] 3 tests from BinAverageModuleTest (20 ms total)
46:
46: [----------] 4 tests from AbstractAverageHistogramTest
46: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
46: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (8 ms)
46: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
46: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (7 ms)
46: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
46: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (7 ms)
46: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
46: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (7 ms)
46: [----------] 4 tests from AbstractAverageHistogramTest (29 ms total)
46:
46: [----------] 3 tests from LifetimeModuleTest
46: [ RUN ] LifetimeModuleTest.BasicTest
46: [ OK ] LifetimeModuleTest.BasicTest (5 ms)
46: [ RUN ] LifetimeModuleTest.CumulativeTest
46: [ OK ] LifetimeModuleTest.CumulativeTest (5 ms)
46: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
46: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (5 ms)
46: [----------] 3 tests from LifetimeModuleTest (16 ms total)
46:
46: [----------] Global test environment tear-down
46: [==========] 69 tests from 14 test cases ran. (284 ms total)
46: [ PASSED ] 69 tests.
46/65 Test #46: AnalysisDataUnitTests ................. Passed 0.36 sec
test 47
Start 47: CoordinateIOTests
47: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml"
47: Test timeout computed to be: 30
47: [==========] Running 64 tests from 19 test cases.
47: [----------] Global test environment set-up.
47: [----------] 1 test from OutputSelectorDeathTest
47: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (36 ms)
47: [----------] 1 test from OutputSelectorDeathTest (37 ms total)
47:
47: [----------] 5 tests from TrajectoryFrameWriterTest
47: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (25 ms)
47: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (24 ms)
47: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (24 ms)
47: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (48 ms)
47: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks
47: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms)
47: [----------] 5 tests from TrajectoryFrameWriterTest (125 ms total)
47:
47: [----------] 5 tests from OutputAdapterContainer
47: [ RUN ] OutputAdapterContainer.MakeEmpty
47: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms)
47: [ RUN ] OutputAdapterContainer.AddAdapter
47: [ OK ] OutputAdapterContainer.AddAdapter (0 ms)
47: [ RUN ] OutputAdapterContainer.RejectBadAdapter
47: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms)
47: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter
47: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms)
47: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters
47: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms)
47: [----------] 5 tests from OutputAdapterContainer (1 ms total)
47:
47: [----------] 5 tests from FlagTest
47: [ RUN ] FlagTest.CanSetSimpleFlag
47: [ OK ] FlagTest.CanSetSimpleFlag (1 ms)
47: [ RUN ] FlagTest.CanAddNewBox
47: [ OK ] FlagTest.CanAddNewBox (0 ms)
47: [ RUN ] FlagTest.SetsImplicitPrecisionChange
47: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms)
47: [ RUN ] FlagTest.SetsImplicitStartTimeChange
47: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms)
47: [ RUN ] FlagTest.SetsImplicitTimeStepChange
47: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms)
47: [----------] 5 tests from FlagTest (3 ms total)
47:
47: [----------] 5 tests from SetAtomsTest
47: [ RUN ] SetAtomsTest.RemovesExistingAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.RemovesExistingAtoms (25 ms)
47: [ RUN ] SetAtomsTest.AddsNewAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.AddsNewAtoms (25 ms)
47: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (25 ms)
47: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (29 ms)
47: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (45 ms)
47: [----------] 5 tests from SetAtomsTest (150 ms total)
47:
47: [----------] 2 tests from SetBothTimeTest
47: [ RUN ] SetBothTimeTest.StartTimeZeroWorks
47: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms)
47: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks
47: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms)
47: [----------] 2 tests from SetBothTimeTest (1 ms total)
47:
47: [----------] 2 tests from SetStartTimeTest
47: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart
47: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms)
47: [ RUN ] SetStartTimeTest.WorksWithZeroStart
47: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms)
47: [----------] 2 tests from SetStartTimeTest (1 ms total)
47:
47: [----------] 1 test from SetTimeStepTest
47: [ RUN ] SetTimeStepTest.SetTimeStepWorks
47: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms)
47: [----------] 1 test from SetTimeStepTest (0 ms total)
47:
47: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (24 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (50 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (25 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (49 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (24 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (29 ms)
47: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (203 ms total)
47:
47: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles
47: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (45 ms)
47: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (25 ms)
47: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (25 ms)
47: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (95 ms total)
47:
47: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms)
47: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (1 ms total)
47:
47: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (51 ms)
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (51 ms)
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (51 ms)
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (51 ms)
47: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (204 ms total)
47:
47: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles
47: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (25 ms)
47: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (25 ms)
47: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (25 ms)
47: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (75 ms total)
47:
47: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (1 ms)
47: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (1 ms)
47: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (2 ms total)
47:
47: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles
47: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (25 ms)
47: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (24 ms)
47: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (50 ms total)
47:
47: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms)
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms)
47: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (2 ms total)
47:
47: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles
47: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (25 ms)
47: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (25 ms)
47: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (50 ms total)
47:
47: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms)
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms)
47: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (2 ms total)
47:
47: [----------] 4 tests from ModuleSupported/NoOptionalOutput
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (25 ms)
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (25 ms)
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (26 ms)
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (25 ms)
47: [----------] 4 tests from ModuleSupported/NoOptionalOutput (101 ms total)
47:
47: [----------] Global test environment tear-down
47: [==========] 64 tests from 19 test cases ran. (1107 ms total)
47: [ PASSED ] 64 tests.
47/65 Test #47: CoordinateIOTests ..................... Passed 1.18 sec
test 48
Start 48: TrajectoryAnalysisUnitTests
48: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
48: Test timeout computed to be: 1920
48: [==========] Running 82 tests from 16 test cases.
48: [----------] Global test environment set-up.
48: [----------] 11 tests from AngleModuleTest
48: [ RUN ] AngleModuleTest.ComputesSimpleAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesSimpleAngles (64 ms)
48: [ RUN ] AngleModuleTest.ComputesDihedrals
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesDihedrals (21 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorPairAngles (34 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (21 ms)
48: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (19 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (19 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
48: Reading frames from gro file 'Test system for different angles', 33 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (22 ms)
48: [ RUN ] AngleModuleTest.ComputesMultipleAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesMultipleAngles (20 ms)
48: [ RUN ] AngleModuleTest.HandlesDynamicSelections
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.HandlesDynamicSelections (18 ms)
48: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (19 ms)
48: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (20 ms)
48: [----------] 11 tests from AngleModuleTest (284 ms total)
48:
48: [----------] 5 tests from ClustsizeTest
48: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
48: There is one group in the index
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 24
48: cmid: 2, cmax: 4, max_size: 6
48: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
48: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (17 ms)
48: [ RUN ] ClustsizeTest.NoMolShortCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
48: There is one group in the index
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 24
48: cmid: 1, cmax: 6, max_size: 6
48: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
48: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (12 ms)
48: [ RUN ] ClustsizeTest.MolDefaultCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 8
48: cmid: 2, cmax: 4, max_size: 2
48: 50%100%cmid: 2, cmax: 6, max_size: 2
48: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (33 ms)
48: [ RUN ] ClustsizeTest.MolShortCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 8
48: cmid: 1, cmax: 6, max_size: 2
48: 50%100%cmid: 2, cmax: 6, max_size: 2
48: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (15 ms)
48: [ RUN ] ClustsizeTest.MolCSize
48: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 8
48: cmid: 2, cmax: 4, max_size: 2
48: 50%100%cmid: 2, cmax: 6, max_size: 2
48: 50%100%[ OK ] ClustsizeTest.MolCSize (16 ms)
48: [----------] 5 tests from ClustsizeTest (94 ms total)
48:
48: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (5 ms)
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
48: Reading frames from gro file 'Test system', 8 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (18 ms)
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
48: Reading frames from gro file 'Test system', 8 atoms.
48:
Reading frame 0 time 0.000
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (17 ms)
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (2 ms)
48: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (43 ms total)
48:
48: [----------] 4 tests from ConvertTrjModuleTest
48: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (96 ms)
48: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (91 ms)
48: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (22 ms)
48: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (15 ms)
48: [----------] 4 tests from ConvertTrjModuleTest (229 ms total)
48:
48: [----------] 3 tests from DistanceModuleTest
48: [ RUN ] DistanceModuleTest.ComputesDistances
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: atomname S1 S2:
48: Number of samples: 5
48: Average distance: 1.43246 nm
48: Standard deviation: 0.96700 nm
48: [ OK ] DistanceModuleTest.ComputesDistances (27 ms)
48: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: atomname S1 S2:
48: Number of samples: 5
48: Average distance: 1.43246 nm
48: Standard deviation: 0.96700 nm
48: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
48: Number of samples: 4
48: Average distance: 1.81066 nm
48: Standard deviation: 0.79289 nm
48: [ OK ] DistanceModuleTest.ComputesMultipleDistances (32 ms)
48: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: atomname S1 S2 and res_cog x < 2.8:
48: Number of samples: 3
48: Average distance: 1.72076 nm
48: Standard deviation: 1.24839 nm
48: [ OK ] DistanceModuleTest.HandlesDynamicSelections (35 ms)
48: [----------] 3 tests from DistanceModuleTest (96 ms total)
48:
48: [----------] 2 tests from ExtractClusterModuleTest
48: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms
48: trr version: GMX_trn_file (single precision)
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
48: Analyzed 26 frames, last time 0.050
48: There are 8 clusters containing 26 structures, highest framenr is 25
48: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (21 ms)
48: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
48: Analyzed 26 frames, last time 0.050
48: There are 8 clusters containing 26 structures, highest framenr is 25
48: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (17 ms)
48: [----------] 2 tests from ExtractClusterModuleTest (38 ms total)
48:
48: [----------] 2 tests from FreeVolumeModuleTest
48: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for 40 particles. These were set to zero.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: cutoff = 0.18 nm
48: probe_radius = 0 nm
48: seed = 13
48: ninsert = 1000 probes per nm^3
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
48: van der Spoel and Luciano T. Costa
48: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
48: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
48: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
48: -------- -------- --- Thank You --- -------- --------
48:
48: Free volume 38.02 +/- 0.00 %
48: Total volume 68.92 +/- 0.00 nm^3
48: Number of molecules 340 total mass 63491.38 Dalton
48: Average molar mass: 186.74 Dalton
48: Density rho: 1529.71 +/- 0.00 nm^3
48: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
48: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
48: Fractional free volume 0.194 +/- 0.000
48: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (703 ms)
48: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: cutoff = 0.18 nm
48: probe_radius = 0 nm
48: seed = 17
48: ninsert = 1000 probes per nm^3
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
48: van der Spoel and Luciano T. Costa
48: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
48: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
48: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
48: -------- -------- --- Thank You --- -------- --------
48:
48: Free volume 38.48 +/- 0.00 %
48: Total volume 68.92 +/- 0.00 nm^3
48: Number of molecules 340 total mass 63491.38 Dalton
48: Average molar mass: 186.74 Dalton
48: Density rho: 1529.71 +/- 0.00 nm^3
48: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
48: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
48: Fractional free volume 0.200 +/- 0.000
48: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (799 ms)
48: [----------] 2 tests from FreeVolumeModuleTest (1503 ms total)
48:
48: [----------] 9 tests from PairDistanceModuleTest
48: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesAllDistances (19 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (20 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (18 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (18 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (18 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (19 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (18 ms)
48: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (18 ms)
48: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (18 ms)
48: [----------] 9 tests from PairDistanceModuleTest (174 ms total)
48:
48: [----------] 5 tests from RdfModuleTest
48: [ RUN ] RdfModuleTest.BasicTest
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.BasicTest (166 ms)
48: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
48: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (107 ms)
48: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (166 ms)
48: [ RUN ] RdfModuleTest.CalculatesSurf
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.CalculatesSurf (100 ms)
48: [ RUN ] RdfModuleTest.CalculatesXY
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.CalculatesXY (214 ms)
48: [----------] 5 tests from RdfModuleTest (757 ms total)
48:
48: [----------] 5 tests from SasaModuleTest
48: [ RUN ] SasaModuleTest.BasicTest
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.BasicTest (119 ms)
48: [ RUN ] SasaModuleTest.HandlesSelectedResidues
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.HandlesSelectedResidues (57 ms)
48: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (66 ms)
48: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (63 ms)
48: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (60 ms)
48: [----------] 5 tests from SasaModuleTest (389 ms total)
48:
48: [----------] 8 tests from SelectModuleTest
48: [ RUN ] SelectModuleTest.BasicTest
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.BasicTest (34 ms)
48: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (26 ms)
48: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (27 ms)
48: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (27 ms)
48: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (26 ms)
48: [ RUN ] SelectModuleTest.NormalizesSizes
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.NormalizesSizes (18 ms)
48: [ RUN ] SelectModuleTest.WritesResidueNumbers
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.WritesResidueNumbers (18 ms)
48: [ RUN ] SelectModuleTest.WritesResidueIndices
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.WritesResidueIndices (18 ms)
48: [----------] 8 tests from SelectModuleTest (202 ms total)
48:
48: [----------] 10 tests from SurfaceAreaTest
48: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
48: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms)
48: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
48: [ OK ] SurfaceAreaTest.ComputesTwoPoints (7 ms)
48: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
48: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (7 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints12
48: [ OK ] SurfaceAreaTest.SurfacePoints12 (2 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints32
48: [ OK ] SurfaceAreaTest.SurfacePoints32 (2 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints42
48: [ OK ] SurfaceAreaTest.SurfacePoints42 (3 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints122
48: [ OK ] SurfaceAreaTest.SurfacePoints122 (6 ms)
48: [ RUN ] SurfaceAreaTest.Computes100Points
48: [ OK ] SurfaceAreaTest.Computes100Points (4 ms)
48: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
48: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (15 ms)
48: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
48: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (17 ms)
48: [----------] 10 tests from SurfaceAreaTest (67 ms total)
48:
48: [----------] 4 tests from TopologyInformation
48: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
48: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms)
48: [ RUN ] TopologyInformation.WorksWithGroFile
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TopologyInformation.WorksWithGroFile (26 ms)
48: [ RUN ] TopologyInformation.WorksWithPdbFile
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TopologyInformation.WorksWithPdbFile (25 ms)
48: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Generating 1-4 interactions: fudge = 0.5
48:
48: NOTE 2 [file lysozyme.top, line 1465]:
48: System has non-zero total charge: 2.000000
48: Total charge should normally be an integer. See
48: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
48: for discussion on how close it should be to an integer.
48:
48:
48:
48: Number of degrees of freedom in T-Coupling group rest is 465.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
48: Setting the LD random seed to -830488867
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48:
48: Generated 330891 of the 330891 1-4 parameter combinations
48:
48: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
48: Analysing residue names:
48: There are: 10 Protein residues
48: Analysing Protein...
48:
48: This run will generate roughly 0 Mb of data
48: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (4666 ms)
48: [----------] 4 tests from TopologyInformation (4718 ms total)
48:
48: [----------] 4 tests from TrajectoryModuleTest
48: [ RUN ] TrajectoryModuleTest.BasicTest
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.BasicTest (46 ms)
48: [ RUN ] TrajectoryModuleTest.PlotsXOnly
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.PlotsXOnly (21 ms)
48: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (28 ms)
48: [ RUN ] TrajectoryModuleTest.HandlesNoForces
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.HandlesNoForces (36 ms)
48: [----------] 4 tests from TrajectoryModuleTest (132 ms total)
48:
48: [----------] 5 tests from UnionFinderTest
48: [ RUN ] UnionFinderTest.WorksEmpty
48: [ OK ] UnionFinderTest.WorksEmpty (0 ms)
48: [ RUN ] UnionFinderTest.BasicMerges
48: [ OK ] UnionFinderTest.BasicMerges (0 ms)
48: [ RUN ] UnionFinderTest.LargerMerges
48: [ OK ] UnionFinderTest.LargerMerges (0 ms)
48: [ RUN ] UnionFinderTest.LongRightMerge
48: [ OK ] UnionFinderTest.LongRightMerge (1 ms)
48: [ RUN ] UnionFinderTest.LongLeftMerge
48: [ OK ] UnionFinderTest.LongLeftMerge (0 ms)
48: [----------] 5 tests from UnionFinderTest (1 ms total)
48:
48: [----------] 1 test from MappedUnionFinderTest
48: [ RUN ] MappedUnionFinderTest.BasicMerges
48: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms)
48: [----------] 1 test from MappedUnionFinderTest (0 ms total)
48:
48: [----------] Global test environment tear-down
48: [==========] 82 tests from 16 test cases ran. (8731 ms total)
48: [ PASSED ] 82 tests.
48/65 Test #48: TrajectoryAnalysisUnitTests ........... Passed 8.82 sec
test 49
Start 49: EnergyAnalysisUnitTests
49: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml"
49: Test timeout computed to be: 30
49: [==========] Running 7 tests from 4 test cases.
49: [----------] Global test environment set-up.
49: [----------] 1 test from DhdlTest
49: [ RUN ] DhdlTest.ExtractDhdl
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
49: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
49: Note: file tpx version 110, software tpx version 122
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
49:
49:
49: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
49: [ OK ] DhdlTest.ExtractDhdl (111 ms)
49: [----------] 1 test from DhdlTest (114 ms total)
49:
49: [----------] 1 test from OriresTest
49: [ RUN ] OriresTest.ExtractOrires
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
49: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
49: Note: file tpx version 111, software tpx version 122
49: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
49: End your selection with 0
49: Selecting all 7 orientation restraints
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
49: [ OK ] OriresTest.ExtractOrires (92 ms)
49: [----------] 1 test from OriresTest (93 ms total)
49:
49: [----------] 3 tests from EnergyTest
49: [ RUN ] EnergyTest.ExtractEnergy
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
49: Select the terms you want from the following list by
49: selecting either (part of) the name or the number or a combination.
49: End your selection with an empty line or a zero.
49: -------------------------------------------------------------------
49: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
49: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
49: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
49: 13 Box-Z 14 Volume 15 Density 16 pV
49: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
49: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
49: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
49: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
49: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
49: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
49:
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
49: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
49: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
49: [ OK ] EnergyTest.ExtractEnergy (23 ms)
49: [ RUN ] EnergyTest.ExtractEnergyByNumber
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
49: Select the terms you want from the following list by
49: selecting either (part of) the name or the number or a combination.
49: End your selection with an empty line or a zero.
49: -------------------------------------------------------------------
49: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
49: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
49: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
49: 13 Box-Z 14 Volume 15 Density 16 pV
49: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
49: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
49: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
49: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
49: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
49: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
49:
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
49: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
49: Pres. DC -268.49 3 8.52175 13.2804 (bar)
49: [ OK ] EnergyTest.ExtractEnergyByNumber (16 ms)
49: [ RUN ] EnergyTest.ExtractEnergyMixed
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
49: Select the terms you want from the following list by
49: selecting either (part of) the name or the number or a combination.
49: End your selection with an empty line or a zero.
49: -------------------------------------------------------------------
49: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
49: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
49: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
49: 13 Box-Z 14 Volume 15 Density 16 pV
49: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
49: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
49: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
49: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
49: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
49: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
49:
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
49: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
49: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
49: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
49: [ OK ] EnergyTest.ExtractEnergyMixed (17 ms)
49: [----------] 3 tests from EnergyTest (59 ms total)
49:
49: [----------] 2 tests from ViscosityTest
49: [ RUN ] ViscosityTest.EinsteinViscosity
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Pres-XX 20.2092 65 717.193 185.978 (bar)
49: Pres-XY -47.7351 39 372.522 207.456 (bar)
49: Pres-XZ 11.477 31 379.79 6.80818 (bar)
49: Pres-YX -47.7106 39 372.525 207.5 (bar)
49: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
49: Pres-YZ -41.3534 45 401.216 114.663 (bar)
49: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
49: Pres-ZY -41.3119 45 401.196 114.743 (bar)
49: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
49: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
49: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
49: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
49: [ OK ] ViscosityTest.EinsteinViscosity (34 ms)
49: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Pres-XX 20.2092 65 717.193 185.978 (bar)
49: Pres-XY -47.7351 39 372.522 207.456 (bar)
49: Pres-XZ 11.477 31 379.79 6.80818 (bar)
49: Pres-YX -47.7106 39 372.525 207.5 (bar)
49: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
49: Pres-YZ -41.3534 45 401.216 114.663 (bar)
49: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
49: Pres-ZY -41.3119 45 401.196 114.743 (bar)
49: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
49: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
49: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
49: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
49: [ OK ] ViscosityTest.EinsteinViscosityIntegral (42 ms)
49: [----------] 2 tests from ViscosityTest (78 ms total)
49:
49: [----------] Global test environment tear-down
49: [==========] 7 tests from 4 test cases ran. (345 ms total)
49: [ PASSED ] 7 tests.
49/65 Test #49: EnergyAnalysisUnitTests ............... Passed 0.41 sec
test 50
Start 50: ToolUnitTests
50: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/ToolUnitTests.xml"
50: Test timeout computed to be: 1920
50: [==========] Running 21 tests from 5 test cases.
50: [----------] Global test environment set-up.
50: [----------] 2 tests from DumpTest
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
50: For a correct single-point energy evaluation with nsteps = 0, use
50: continuation = yes to avoid constraining the input coordinates.
50:
50: Generating 1-4 interactions: fudge = 0.5
50:
50: NOTE 2 [file lysozyme.top, line 1465]:
50: System has non-zero total charge: 2.000000
50: Total charge should normally be an integer. See
50: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
50: for discussion on how close it should be to an integer.
50:
50:
50:
50: Number of degrees of freedom in T-Coupling group rest is 465.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
50: NVE simulation with an initial temperature of zero: will use a Verlet
50: buffer of 10%. Check your energy drift!
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Setting the LD random seed to 1773886651
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50:
50: Generated 330891 of the 330891 1-4 parameter combinations
50:
50: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
50: Analysing residue names:
50: There are: 10 Protein residues
50: Analysing Protein...
50:
50: This run will generate roughly 0 Mb of data
50: [ RUN ] DumpTest.WorksWithTpr
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
50: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr:
50: inputrec:
50: integrator = md
50: tinit = 0
50: dt = 0.001
50: nsteps = 0
50: init-step = 0
50: simulation-part = 1
50: mts = false
50: comm-mode = Linear
50: nstcomm = 100
50: bd-fric = 0
50: ld-seed = 1773886651
50: emtol = 10
50: emstep = 0.01
50: niter = 20
50: fcstep = 0
50: nstcgsteep = 1000
50: nbfgscorr = 10
50: rtpi = 0.05
50: nstxout = 0
50: nstvout = 0
50: nstfout = 0
50: nstlog = 1000
50: nstcalcenergy = 100
50: nstenergy = 1000
50: nstxout-compressed = 0
50: compressed-x-precision = 1000
50: cutoff-scheme = Verlet
50: nstlist = 10
50: pbc = xyz
50: periodic-molecules = false
50: verlet-buffer-tolerance = -1
50: rlist = 1.1
50: coulombtype = Cut-off
50: coulomb-modifier = Potential-shift
50: rcoulomb-switch = 0
50: rcoulomb = 1
50: epsilon-r = 1
50: epsilon-rf = inf
50: vdw-type = Cut-off
50: vdw-modifier = Potential-shift
50: rvdw-switch = 0
50: rvdw = 1
50: DispCorr = No
50: table-extension = 1
50: fourierspacing = 0.12
50: fourier-nx = 0
50: fourier-ny = 0
50: fourier-nz = 0
50: pme-order = 4
50: ewald-rtol = 1e-05
50: ewald-rtol-lj = 0.001
50: lj-pme-comb-rule = Geometric
50: ewald-geometry = 0
50: epsilon-surface = 0
50: tcoupl = No
50: nsttcouple = -1
50: nh-chain-length = 0
50: print-nose-hoover-chain-variables = false
50: pcoupl = No
50: pcoupltype = Isotropic
50: nstpcouple = -1
50: tau-p = 1
50: compressibility (3x3):
50: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: ref-p (3x3):
50: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: refcoord-scaling = No
50: posres-com (3):
50: posres-com[0]= 0.00000e+00
50: posres-com[1]= 0.00000e+00
50: posres-com[2]= 0.00000e+00
50: posres-comB (3):
50: posres-comB[0]= 0.00000e+00
50: posres-comB[1]= 0.00000e+00
50: posres-comB[2]= 0.00000e+00
50: QMMM = false
50: qm-opts:
50: ngQM = 0
50: constraint-algorithm = Lincs
50: continuation = false
50: Shake-SOR = false
50: shake-tol = 0.0001
50: lincs-order = 4
50: lincs-iter = 1
50: lincs-warnangle = 30
50: nwall = 0
50: wall-type = 9-3
50: wall-r-linpot = -1
50: wall-atomtype[0] = -1
50: wall-atomtype[1] = -1
50: wall-density[0] = 0
50: wall-density[1] = 0
50: wall-ewald-zfac = 3
50: pull = false
50: awh = false
50: rotation = false
50: interactiveMD = false
50: disre = No
50: disre-weighting = Conservative
50: disre-mixed = false
50: dr-fc = 1000
50: dr-tau = 0
50: nstdisreout = 100
50: orire-fc = 0
50: orire-tau = 0
50: nstorireout = 100
50: free-energy = no
50: cos-acceleration = 0
50: deform (3x3):
50: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: simulated-tempering = false
50: swapcoords = no
50: userint1 = 0
50: userint2 = 0
50: userint3 = 0
50: userint4 = 0
50: userreal1 = 0
50: userreal2 = 0
50: userreal3 = 0
50: userreal4 = 0
50: applied-forces:
50: electric-field:
50: x:
50: E0 = 0
50: omega = 0
50: t0 = 0
50: sigma = 0
50: y:
50: E0 = 0
50: omega = 0
50: t0 = 0
50: sigma = 0
50: z:
50: E0 = 0
50: omega = 0
50: t0 = 0
50: sigma = 0
50: density-guided-simulation:
50: active = false
50: group = protein
50: similarity-measure = inner-product
50: atom-spreading-weight = unity
50: force-constant = 1e+09
50: gaussian-transform-spreading-width = 0.2
50: gaussian-transform-spreading-range-in-multiples-of-width = 4
50: reference-density-filename = reference.mrc
50: nst = 1
50: normalize-densities = true
50: adaptive-force-scaling = false
50: adaptive-force-scaling-time-constant = 4
50: shift-vector =
50: transformation-matrix =
50: grpopts:
50: nrdf: 465
50: ref-t: 0
50: tau-t: 0
50: annealing: No
50: annealing-npoints: 0
50: acc: 0 0 0
50: nfreeze: N N N
50: energygrp-flags[ 0]: 0
50: header:
50: bIr = present
50: bBox = present
50: bTop = present
50: bX = present
50: bV = present
50: bF = not present
50: natoms = 156
50: lambda = 0.000000e+00
50: buffer size = 70158
50: topology:
50: name="First 10 residues from 1AKI"
50: #atoms = 156
50: #molblock = 1
50: molblock (0):
50: moltype = 0 "Protein_chain_B"
50: #molecules = 1
50: #posres_xA = 0
50: #posres_xB = 0
50: bIntermolecularInteractions = false
50: ffparams:
50: atnr=10
50: ntypes=212
50: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06
50: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06
50: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07
50: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06
50: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06
50: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06
50: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07
50: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07
50: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05
50: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06
50: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06
50: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07
50: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06
50: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06
50: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06
50: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07
50: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07
50: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05
50: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07
50: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07
50: functype[33]=LJ_SR, c6= 1.22578125e-04, c12= 2.99263000e-08
50: functype[34]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07
50: functype[35]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07
50: functype[36]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07
50: functype[37]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08
50: functype[38]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08
50: functype[39]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06
50: functype[40]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06
50: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[42]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06
50: functype[43]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07
50: functype[44]=LJ_SR, c6= 4.88684509e-03, c12= 1.35898974e-05
50: functype[45]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06
50: functype[46]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06
50: functype[47]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07
50: functype[48]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07
50: functype[49]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05
50: functype[50]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06
50: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[52]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06
50: functype[53]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07
50: functype[54]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06
50: functype[55]=LJ_SR, c6= 2.36385715e-03, c12= 1.58990617e-06
50: functype[56]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06
50: functype[57]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07
50: functype[58]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07
50: functype[59]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06
50: functype[60]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06
50: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[62]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06
50: functype[63]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07
50: functype[64]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06
50: functype[65]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06
50: functype[66]=LJ_SR, c6= 2.34487570e-03, c12= 4.69342567e-06
50: functype[67]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07
50: functype[68]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07
50: functype[69]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05
50: functype[70]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07
50: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[72]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07
50: functype[73]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08
50: functype[74]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07
50: functype[75]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07
50: functype[76]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07
50: functype[77]=LJ_SR, c6= 1.00847496e-04, c12= 2.02561691e-08
50: functype[78]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08
50: functype[79]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07
50: functype[80]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07
50: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[82]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07
50: functype[83]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08
50: functype[84]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07
50: functype[85]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07
50: functype[86]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07
50: functype[87]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08
50: functype[88]=LJ_SR, c6= 1.08571736e-04, c12= 1.40867851e-08
50: functype[89]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07
50: functype[90]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05
50: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[92]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05
50: functype[93]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06
50: functype[94]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05
50: functype[95]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06
50: functype[96]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05
50: functype[97]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07
50: functype[98]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07
50: functype[99]=LJ_SR, c6= 1.54830174e-02, c12= 3.37031588e-05
50: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05
50: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05
50: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05
50: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05
50: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05
50: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05
50: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05
50: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05
50: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05
50: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05
50: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05
50: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05
50: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05
50: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05
50: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05
50: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05
50: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02
50: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02
50: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02
50: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02
50: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02
50: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02
50: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02
50: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02
50: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02
50: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02
50: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02
50: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02
50: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02
50: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02
50: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02
50: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02
50: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02
50: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02
50: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02
50: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02
50: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02
50: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02
50: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02
50: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02
50: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2
50: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2
50: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2
50: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07
50: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06
50: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06
50: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06
50: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00
50: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07
50: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06
50: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08
50: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07
50: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06
50: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07
50: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06
50: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06
50: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06
50: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06
50: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07
50: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07
50: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07
50: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06
50: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06
50: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08
50: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07
50: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08
50: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06
50: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07
50: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05
50: reppow = 12
50: fudgeQQ = 0.5
50: cmap
50: atomtypes:
50: atomtype[ 0]={atomnumber= 7}
50: atomtype[ 1]={atomnumber= 1}
50: atomtype[ 2]={atomnumber= 6}
50: atomtype[ 3]={atomnumber= 1}
50: atomtype[ 4]={atomnumber= 6}
50: atomtype[ 5]={atomnumber= 8}
50: atomtype[ 6]={atomnumber= 6}
50: atomtype[ 7]={atomnumber= 1}
50: atomtype[ 8]={atomnumber= 6}
50: atomtype[ 9]={atomnumber= 16}
50: moltype (0):
50: name="Protein_chain_B"
50: atoms:
50: atom (156):
50: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
50: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6}
50: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
50: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
50: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
50: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6}
50: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
50: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6}
50: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8}
50: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7}
50: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1}
50: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6}
50: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6}
50: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
50: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
50: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6}
50: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8}
50: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7}
50: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1}
50: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6}
50: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
50: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6}
50: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
50: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
50: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6}
50: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8}
50: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7}
50: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1}
50: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6}
50: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
50: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
50: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6}
50: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8}
50: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1}
50: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6}
50: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6}
50: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6}
50: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6}
50: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1}
50: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6}
50: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6}
50: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8}
50: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7}
50: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1}
50: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6}
50: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
50: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6}
50: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
50: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
50: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16}
50: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1}
50: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6}
50: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8}
50: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7}
50: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1}
50: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6}
50: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6}
50: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6}
50: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6}
50: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
50: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
50: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6}
50: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8}
50: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7}
50: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1}
50: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6}
50: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6}
50: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6}
50: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
50: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
50: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6}
50: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8}
50: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7}
50: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1}
50: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6}
50: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6}
50: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6}
50: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8}
50: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7}
50: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1}
50: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6}
50: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6}
50: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6}
50: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8}
50: atom (156):
50: atom[0]={name="N"}
50: atom[1]={name="H1"}
50: atom[2]={name="H2"}
50: atom[3]={name="H3"}
50: atom[4]={name="CA"}
50: atom[5]={name="HA"}
50: atom[6]={name="CB"}
50: atom[7]={name="HB1"}
50: atom[8]={name="HB2"}
50: atom[9]={name="CG"}
50: atom[10]={name="HG1"}
50: atom[11]={name="HG2"}
50: atom[12]={name="CD"}
50: atom[13]={name="HD1"}
50: atom[14]={name="HD2"}
50: atom[15]={name="CE"}
50: atom[16]={name="HE1"}
50: atom[17]={name="HE2"}
50: atom[18]={name="NZ"}
50: atom[19]={name="HZ1"}
50: atom[20]={name="HZ2"}
50: atom[21]={name="HZ3"}
50: atom[22]={name="C"}
50: atom[23]={name="O"}
50: atom[24]={name="N"}
50: atom[25]={name="H"}
50: atom[26]={name="CA"}
50: atom[27]={name="HA"}
50: atom[28]={name="CB"}
50: atom[29]={name="HB"}
50: atom[30]={name="CG1"}
50: atom[31]={name="HG11"}
50: atom[32]={name="HG12"}
50: atom[33]={name="HG13"}
50: atom[34]={name="CG2"}
50: atom[35]={name="HG21"}
50: atom[36]={name="HG22"}
50: atom[37]={name="HG23"}
50: atom[38]={name="C"}
50: atom[39]={name="O"}
50: atom[40]={name="N"}
50: atom[41]={name="H"}
50: atom[42]={name="CA"}
50: atom[43]={name="HA"}
50: atom[44]={name="CB"}
50: atom[45]={name="HB1"}
50: atom[46]={name="HB2"}
50: atom[47]={name="CG"}
50: atom[48]={name="CD1"}
50: atom[49]={name="HD1"}
50: atom[50]={name="CD2"}
50: atom[51]={name="HD2"}
50: atom[52]={name="CE1"}
50: atom[53]={name="HE1"}
50: atom[54]={name="CE2"}
50: atom[55]={name="HE2"}
50: atom[56]={name="CZ"}
50: atom[57]={name="HZ"}
50: atom[58]={name="C"}
50: atom[59]={name="O"}
50: atom[60]={name="N"}
50: atom[61]={name="H"}
50: atom[62]={name="CA"}
50: atom[63]={name="HA1"}
50: atom[64]={name="HA2"}
50: atom[65]={name="C"}
50: atom[66]={name="O"}
50: atom[67]={name="N"}
50: atom[68]={name="H"}
50: atom[69]={name="CA"}
50: atom[70]={name="HA"}
50: atom[71]={name="CB"}
50: atom[72]={name="HB1"}
50: atom[73]={name="HB2"}
50: atom[74]={name="CG"}
50: atom[75]={name="HG1"}
50: atom[76]={name="HG2"}
50: atom[77]={name="CD"}
50: atom[78]={name="HD1"}
50: atom[79]={name="HD2"}
50: atom[80]={name="NE"}
50: atom[81]={name="HE"}
50: atom[82]={name="CZ"}
50: atom[83]={name="NH1"}
50: atom[84]={name="HH11"}
50: atom[85]={name="HH12"}
50: atom[86]={name="NH2"}
50: atom[87]={name="HH21"}
50: atom[88]={name="HH22"}
50: atom[89]={name="C"}
50: atom[90]={name="O"}
50: atom[91]={name="N"}
50: atom[92]={name="H"}
50: atom[93]={name="CA"}
50: atom[94]={name="HA"}
50: atom[95]={name="CB"}
50: atom[96]={name="HB1"}
50: atom[97]={name="HB2"}
50: atom[98]={name="SG"}
50: atom[99]={name="HG"}
50: atom[100]={name="C"}
50: atom[101]={name="O"}
50: atom[102]={name="N"}
50: atom[103]={name="H"}
50: atom[104]={name="CA"}
50: atom[105]={name="HA"}
50: atom[106]={name="CB"}
50: atom[107]={name="HB1"}
50: atom[108]={name="HB2"}
50: atom[109]={name="CG"}
50: atom[110]={name="HG1"}
50: atom[111]={name="HG2"}
50: atom[112]={name="CD"}
50: atom[113]={name="OE1"}
50: atom[114]={name="OE2"}
50: atom[115]={name="C"}
50: atom[116]={name="O"}
50: atom[117]={name="N"}
50: atom[118]={name="H"}
50: atom[119]={name="CA"}
50: atom[120]={name="HA"}
50: atom[121]={name="CB"}
50: atom[122]={name="HB1"}
50: atom[123]={name="HB2"}
50: atom[124]={name="CG"}
50: atom[125]={name="HG"}
50: atom[126]={name="CD1"}
50: atom[127]={name="HD11"}
50: atom[128]={name="HD12"}
50: atom[129]={name="HD13"}
50: atom[130]={name="CD2"}
50: atom[131]={name="HD21"}
50: atom[132]={name="HD22"}
50: atom[133]={name="HD23"}
50: atom[134]={name="C"}
50: atom[135]={name="O"}
50: atom[136]={name="N"}
50: atom[137]={name="H"}
50: atom[138]={name="CA"}
50: atom[139]={name="HA"}
50: atom[140]={name="CB"}
50: atom[141]={name="HB1"}
50: atom[142]={name="HB2"}
50: atom[143]={name="HB3"}
50: atom[144]={name="C"}
50: atom[145]={name="O"}
50: atom[146]={name="N"}
50: atom[147]={name="H"}
50: atom[148]={name="CA"}
50: atom[149]={name="HA"}
50: atom[150]={name="CB"}
50: atom[151]={name="HB1"}
50: atom[152]={name="HB2"}
50: atom[153]={name="HB3"}
50: atom[154]={name="C"}
50: atom[155]={name="O"}
50: type (156):
50: type[0]={name="opls_287",nameB="opls_287"}
50: type[1]={name="opls_290",nameB="opls_290"}
50: type[2]={name="opls_290",nameB="opls_290"}
50: type[3]={name="opls_290",nameB="opls_290"}
50: type[4]={name="opls_293B",nameB="opls_293B"}
50: type[5]={name="opls_140",nameB="opls_140"}
50: type[6]={name="opls_136",nameB="opls_136"}
50: type[7]={name="opls_140",nameB="opls_140"}
50: type[8]={name="opls_140",nameB="opls_140"}
50: type[9]={name="opls_136",nameB="opls_136"}
50: type[10]={name="opls_140",nameB="opls_140"}
50: type[11]={name="opls_140",nameB="opls_140"}
50: type[12]={name="opls_136",nameB="opls_136"}
50: type[13]={name="opls_140",nameB="opls_140"}
50: type[14]={name="opls_140",nameB="opls_140"}
50: type[15]={name="opls_292",nameB="opls_292"}
50: type[16]={name="opls_140",nameB="opls_140"}
50: type[17]={name="opls_140",nameB="opls_140"}
50: type[18]={name="opls_287",nameB="opls_287"}
50: type[19]={name="opls_290",nameB="opls_290"}
50: type[20]={name="opls_290",nameB="opls_290"}
50: type[21]={name="opls_290",nameB="opls_290"}
50: type[22]={name="opls_235",nameB="opls_235"}
50: type[23]={name="opls_236",nameB="opls_236"}
50: type[24]={name="opls_238",nameB="opls_238"}
50: type[25]={name="opls_241",nameB="opls_241"}
50: type[26]={name="opls_224B",nameB="opls_224B"}
50: type[27]={name="opls_140",nameB="opls_140"}
50: type[28]={name="opls_137",nameB="opls_137"}
50: type[29]={name="opls_140",nameB="opls_140"}
50: type[30]={name="opls_135",nameB="opls_135"}
50: type[31]={name="opls_140",nameB="opls_140"}
50: type[32]={name="opls_140",nameB="opls_140"}
50: type[33]={name="opls_140",nameB="opls_140"}
50: type[34]={name="opls_135",nameB="opls_135"}
50: type[35]={name="opls_140",nameB="opls_140"}
50: type[36]={name="opls_140",nameB="opls_140"}
50: type[37]={name="opls_140",nameB="opls_140"}
50: type[38]={name="opls_235",nameB="opls_235"}
50: type[39]={name="opls_236",nameB="opls_236"}
50: type[40]={name="opls_238",nameB="opls_238"}
50: type[41]={name="opls_241",nameB="opls_241"}
50: type[42]={name="opls_224B",nameB="opls_224B"}
50: type[43]={name="opls_140",nameB="opls_140"}
50: type[44]={name="opls_149",nameB="opls_149"}
50: type[45]={name="opls_140",nameB="opls_140"}
50: type[46]={name="opls_140",nameB="opls_140"}
50: type[47]={name="opls_145",nameB="opls_145"}
50: type[48]={name="opls_145",nameB="opls_145"}
50: type[49]={name="opls_146",nameB="opls_146"}
50: type[50]={name="opls_145",nameB="opls_145"}
50: type[51]={name="opls_146",nameB="opls_146"}
50: type[52]={name="opls_145",nameB="opls_145"}
50: type[53]={name="opls_146",nameB="opls_146"}
50: type[54]={name="opls_145",nameB="opls_145"}
50: type[55]={name="opls_146",nameB="opls_146"}
50: type[56]={name="opls_145",nameB="opls_145"}
50: type[57]={name="opls_146",nameB="opls_146"}
50: type[58]={name="opls_235",nameB="opls_235"}
50: type[59]={name="opls_236",nameB="opls_236"}
50: type[60]={name="opls_238",nameB="opls_238"}
50: type[61]={name="opls_241",nameB="opls_241"}
50: type[62]={name="opls_223B",nameB="opls_223B"}
50: type[63]={name="opls_140",nameB="opls_140"}
50: type[64]={name="opls_140",nameB="opls_140"}
50: type[65]={name="opls_235",nameB="opls_235"}
50: type[66]={name="opls_236",nameB="opls_236"}
50: type[67]={name="opls_238",nameB="opls_238"}
50: type[68]={name="opls_241",nameB="opls_241"}
50: type[69]={name="opls_224B",nameB="opls_224B"}
50: type[70]={name="opls_140",nameB="opls_140"}
50: type[71]={name="opls_136",nameB="opls_136"}
50: type[72]={name="opls_140",nameB="opls_140"}
50: type[73]={name="opls_140",nameB="opls_140"}
50: type[74]={name="opls_308",nameB="opls_308"}
50: type[75]={name="opls_140",nameB="opls_140"}
50: type[76]={name="opls_140",nameB="opls_140"}
50: type[77]={name="opls_307",nameB="opls_307"}
50: type[78]={name="opls_140",nameB="opls_140"}
50: type[79]={name="opls_140",nameB="opls_140"}
50: type[80]={name="opls_303",nameB="opls_303"}
50: type[81]={name="opls_304",nameB="opls_304"}
50: type[82]={name="opls_302",nameB="opls_302"}
50: type[83]={name="opls_300",nameB="opls_300"}
50: type[84]={name="opls_301",nameB="opls_301"}
50: type[85]={name="opls_301",nameB="opls_301"}
50: type[86]={name="opls_300",nameB="opls_300"}
50: type[87]={name="opls_301",nameB="opls_301"}
50: type[88]={name="opls_301",nameB="opls_301"}
50: type[89]={name="opls_235",nameB="opls_235"}
50: type[90]={name="opls_236",nameB="opls_236"}
50: type[91]={name="opls_238",nameB="opls_238"}
50: type[92]={name="opls_241",nameB="opls_241"}
50: type[93]={name="opls_224B",nameB="opls_224B"}
50: type[94]={name="opls_140",nameB="opls_140"}
50: type[95]={name="opls_206",nameB="opls_206"}
50: type[96]={name="opls_140",nameB="opls_140"}
50: type[97]={name="opls_140",nameB="opls_140"}
50: type[98]={name="opls_200",nameB="opls_200"}
50: type[99]={name="opls_204",nameB="opls_204"}
50: type[100]={name="opls_235",nameB="opls_235"}
50: type[101]={name="opls_236",nameB="opls_236"}
50: type[102]={name="opls_238",nameB="opls_238"}
50: type[103]={name="opls_241",nameB="opls_241"}
50: type[104]={name="opls_224B",nameB="opls_224B"}
50: type[105]={name="opls_140",nameB="opls_140"}
50: type[106]={name="opls_136",nameB="opls_136"}
50: type[107]={name="opls_140",nameB="opls_140"}
50: type[108]={name="opls_140",nameB="opls_140"}
50: type[109]={name="opls_274",nameB="opls_274"}
50: type[110]={name="opls_140",nameB="opls_140"}
50: type[111]={name="opls_140",nameB="opls_140"}
50: type[112]={name="opls_271",nameB="opls_271"}
50: type[113]={name="opls_272",nameB="opls_272"}
50: type[114]={name="opls_272",nameB="opls_272"}
50: type[115]={name="opls_235",nameB="opls_235"}
50: type[116]={name="opls_236",nameB="opls_236"}
50: type[117]={name="opls_238",nameB="opls_238"}
50: type[118]={name="opls_241",nameB="opls_241"}
50: type[119]={name="opls_224B",nameB="opls_224B"}
50: type[120]={name="opls_140",nameB="opls_140"}
50: type[121]={name="opls_136",nameB="opls_136"}
50: type[122]={name="opls_140",nameB="opls_140"}
50: type[123]={name="opls_140",nameB="opls_140"}
50: type[124]={name="opls_137",nameB="opls_137"}
50: type[125]={name="opls_140",nameB="opls_140"}
50: type[126]={name="opls_135",nameB="opls_135"}
50: type[127]={name="opls_140",nameB="opls_140"}
50: type[128]={name="opls_140",nameB="opls_140"}
50: type[129]={name="opls_140",nameB="opls_140"}
50: type[130]={name="opls_135",nameB="opls_135"}
50: type[131]={name="opls_140",nameB="opls_140"}
50: type[132]={name="opls_140",nameB="opls_140"}
50: type[133]={name="opls_140",nameB="opls_140"}
50: type[134]={name="opls_235",nameB="opls_235"}
50: type[135]={name="opls_236",nameB="opls_236"}
50: type[136]={name="opls_238",nameB="opls_238"}
50: type[137]={name="opls_241",nameB="opls_241"}
50: type[138]={name="opls_224B",nameB="opls_224B"}
50: type[139]={name="opls_140",nameB="opls_140"}
50: type[140]={name="opls_135",nameB="opls_135"}
50: type[141]={name="opls_140",nameB="opls_140"}
50: type[142]={name="opls_140",nameB="opls_140"}
50: type[143]={name="opls_140",nameB="opls_140"}
50: type[144]={name="opls_235",nameB="opls_235"}
50: type[145]={name="opls_236",nameB="opls_236"}
50: type[146]={name="opls_238",nameB="opls_238"}
50: type[147]={name="opls_241",nameB="opls_241"}
50: type[148]={name="opls_224B",nameB="opls_224B"}
50: type[149]={name="opls_140",nameB="opls_140"}
50: type[150]={name="opls_135",nameB="opls_135"}
50: type[151]={name="opls_140",nameB="opls_140"}
50: type[152]={name="opls_140",nameB="opls_140"}
50: type[153]={name="opls_140",nameB="opls_140"}
50: type[154]={name="opls_235",nameB="opls_235"}
50: type[155]={name="opls_236",nameB="opls_236"}
50: residue (10):
50: residue[0]={name="LYS", nr=1, ic=' '}
50: residue[1]={name="VAL", nr=2, ic=' '}
50: residue[2]={name="PHE", nr=3, ic=' '}
50: residue[3]={name="GLY", nr=4, ic=' '}
50: residue[4]={name="ARG", nr=5, ic=' '}
50: residue[5]={name="CYS", nr=6, ic=' '}
50: residue[6]={name="GLU", nr=7, ic=' '}
50: residue[7]={name="LEU", nr=8, ic=' '}
50: residue[8]={name="ALA", nr=9, ic=' '}
50: residue[9]={name="ALA", nr=10, ic=' '}
50: excls:
50: numLists=156
50: numElements=1828
50: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
50: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22}
50: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22}
50: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22}
50: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22,
50: 23, 24, 25, 26}
50: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
50: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
50: 14, 15, 22, 23, 24}
50: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
50: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
50: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
50: 16, 17, 18, 22}
50: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
50: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
50: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
50: 17, 18, 19, 20, 21}
50: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
50: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
50: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
50: 20, 21}
50: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
50: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
50: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
50: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21}
50: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21}
50: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21}
50: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25,
50: 26, 27, 28, 38}
50: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26}
50: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29,
50: 30, 34, 38, 39, 40}
50: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38}
50: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
50: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42}
50: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
50: 40}
50: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
50: 34, 35, 36, 37, 38, 39, 40}
50: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
50: 36, 37, 38}
50: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
50: 36, 37, 38}
50: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34}
50: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34}
50: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34}
50: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
50: 36, 37, 38}
50: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37}
50: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37}
50: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37}
50: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
50: 40, 41, 42, 43, 44, 58}
50: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42}
50: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44,
50: 45, 46, 47, 58, 59, 60}
50: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58}
50: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
50: 48, 50, 58, 59, 60, 61, 62}
50: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
50: 60}
50: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
50: 50, 51, 52, 54, 58, 59, 60}
50: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
50: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
50: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
50: 52, 53, 54, 55, 56, 58}
50: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
50: 54, 56, 57}
50: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56}
50: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54,
50: 55, 56, 57}
50: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56}
50: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57}
50: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57}
50: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57}
50: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57}
50: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57}
50: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57}
50: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
50: 60, 61, 62, 63, 64, 65}
50: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62}
50: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64,
50: 65, 66, 67}
50: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65}
50: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
50: 68, 69}
50: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67}
50: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67}
50: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
50: 70, 71, 89}
50: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69}
50: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
50: 72, 73, 74, 89, 90, 91}
50: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89}
50: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
50: 75, 76, 77, 89, 90, 91, 92, 93}
50: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
50: 91}
50: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
50: 77, 78, 79, 80, 89, 90, 91}
50: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
50: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
50: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
50: 79, 80, 81, 82, 89}
50: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
50: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
50: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
50: 81, 82, 83, 86}
50: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
50: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
50: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,
50: 84, 85, 86, 87, 88}
50: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86}
50: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86,
50: 87, 88}
50: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
50: excls[84][num=6]={80, 82, 83, 84, 85, 86}
50: excls[85][num=6]={80, 82, 83, 84, 85, 86}
50: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
50: excls[87][num=6]={80, 82, 83, 86, 87, 88}
50: excls[88][num=6]={80, 82, 83, 86, 87, 88}
50: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
50: 91, 92, 93, 94, 95, 100}
50: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93}
50: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95,
50: 96, 97, 98, 100, 101, 102}
50: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100}
50: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98,
50: 99, 100, 101, 102, 103, 104}
50: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101,
50: 102}
50: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100,
50: 101, 102}
50: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100}
50: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100}
50: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100}
50: excls[99][num=6]={93, 95, 96, 97, 98, 99}
50: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101,
50: 102, 103, 104, 105, 106, 115}
50: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104}
50: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105,
50: 106, 107, 108, 109, 115, 116, 117}
50: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115}
50: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107,
50: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119}
50: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109,
50: 115, 116, 117}
50: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109,
50: 110, 111, 112, 113, 114, 115, 116, 117}
50: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111,
50: 112, 115}
50: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111,
50: 112, 115}
50: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111,
50: 112, 113, 114, 115}
50: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113,
50: 114}
50: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113,
50: 114}
50: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113,
50: 114}
50: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114}
50: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114}
50: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109,
50: 115, 116, 117, 118, 119, 120, 121, 134}
50: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119}
50: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119,
50: 120, 121, 122, 123, 124, 134, 135, 136}
50: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134}
50: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122,
50: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138}
50: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124,
50: 134, 135, 136}
50: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124,
50: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136}
50: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126,
50: 130, 134}
50: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126,
50: 130, 134}
50: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126,
50: 127, 128, 129, 130, 131, 132, 133, 134}
50: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128,
50: 129, 130, 131, 132, 133}
50: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128,
50: 129, 130, 131, 132, 133}
50: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130}
50: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130}
50: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130}
50: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128,
50: 129, 130, 131, 132, 133}
50: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133}
50: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133}
50: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133}
50: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124,
50: 134, 135, 136, 137, 138, 139, 140, 144}
50: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138}
50: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138,
50: 139, 140, 141, 142, 143, 144, 145, 146}
50: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144}
50: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141,
50: 142, 143, 144, 145, 146, 147, 148}
50: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143,
50: 144, 145, 146}
50: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143,
50: 144, 145, 146}
50: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144}
50: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144}
50: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144}
50: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143,
50: 144, 145, 146, 147, 148, 149, 150, 154}
50: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148}
50: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148,
50: 149, 150, 151, 152, 153, 154, 155}
50: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154}
50: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151,
50: 152, 153, 154, 155}
50: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153,
50: 154, 155}
50: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153,
50: 154, 155}
50: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154}
50: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154}
50: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154}
50: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153,
50: 154, 155}
50: excls[155][num=6]={146, 148, 149, 150, 154, 155}
50: Bond:
50: nr: 468
50: iatoms:
50: 0 type=100 (BONDS) 0 1
50: 1 type=100 (BONDS) 0 2
50: 2 type=100 (BONDS) 0 3
50: 3 type=101 (BONDS) 0 4
50: 4 type=102 (BONDS) 4 5
50: 5 type=103 (BONDS) 4 6
50: 6 type=104 (BONDS) 4 22
50: 7 type=102 (BONDS) 6 7
50: 8 type=102 (BONDS) 6 8
50: 9 type=103 (BONDS) 6 9
50: 10 type=102 (BONDS) 9 10
50: 11 type=102 (BONDS) 9 11
50: 12 type=103 (BONDS) 9 12
50: 13 type=102 (BONDS) 12 13
50: 14 type=102 (BONDS) 12 14
50: 15 type=103 (BONDS) 12 15
50: 16 type=102 (BONDS) 15 16
50: 17 type=102 (BONDS) 15 17
50: 18 type=101 (BONDS) 15 18
50: 19 type=100 (BONDS) 18 19
50: 20 type=100 (BONDS) 18 20
50: 21 type=100 (BONDS) 18 21
50: 22 type=105 (BONDS) 22 23
50: 23 type=106 (BONDS) 22 24
50: 24 type=100 (BONDS) 24 25
50: 25 type=107 (BONDS) 24 26
50: 26 type=102 (BONDS) 26 27
50: 27 type=103 (BONDS) 26 28
50: 28 type=104 (BONDS) 26 38
50: 29 type=102 (BONDS) 28 29
50: 30 type=103 (BONDS) 28 30
50: 31 type=103 (BONDS) 28 34
50: 32 type=102 (BONDS) 30 31
50: 33 type=102 (BONDS) 30 32
50: 34 type=102 (BONDS) 30 33
50: 35 type=102 (BONDS) 34 35
50: 36 type=102 (BONDS) 34 36
50: 37 type=102 (BONDS) 34 37
50: 38 type=105 (BONDS) 38 39
50: 39 type=106 (BONDS) 38 40
50: 40 type=100 (BONDS) 40 41
50: 41 type=107 (BONDS) 40 42
50: 42 type=102 (BONDS) 42 43
50: 43 type=103 (BONDS) 42 44
50: 44 type=104 (BONDS) 42 58
50: 45 type=102 (BONDS) 44 45
50: 46 type=102 (BONDS) 44 46
50: 47 type=108 (BONDS) 44 47
50: 48 type=109 (BONDS) 47 48
50: 49 type=109 (BONDS) 47 50
50: 50 type=110 (BONDS) 48 49
50: 51 type=109 (BONDS) 48 52
50: 52 type=110 (BONDS) 50 51
50: 53 type=109 (BONDS) 50 54
50: 54 type=110 (BONDS) 52 53
50: 55 type=109 (BONDS) 52 56
50: 56 type=110 (BONDS) 54 55
50: 57 type=109 (BONDS) 54 56
50: 58 type=110 (BONDS) 56 57
50: 59 type=105 (BONDS) 58 59
50: 60 type=106 (BONDS) 58 60
50: 61 type=100 (BONDS) 60 61
50: 62 type=107 (BONDS) 60 62
50: 63 type=102 (BONDS) 62 63
50: 64 type=102 (BONDS) 62 64
50: 65 type=104 (BONDS) 62 65
50: 66 type=105 (BONDS) 65 66
50: 67 type=106 (BONDS) 65 67
50: 68 type=100 (BONDS) 67 68
50: 69 type=107 (BONDS) 67 69
50: 70 type=102 (BONDS) 69 70
50: 71 type=103 (BONDS) 69 71
50: 72 type=104 (BONDS) 69 89
50: 73 type=102 (BONDS) 71 72
50: 74 type=102 (BONDS) 71 73
50: 75 type=103 (BONDS) 71 74
50: 76 type=102 (BONDS) 74 75
50: 77 type=102 (BONDS) 74 76
50: 78 type=103 (BONDS) 74 77
50: 79 type=102 (BONDS) 77 78
50: 80 type=102 (BONDS) 77 79
50: 81 type=111 (BONDS) 77 80
50: 82 type=100 (BONDS) 80 81
50: 83 type=112 (BONDS) 80 82
50: 84 type=112 (BONDS) 82 83
50: 85 type=112 (BONDS) 82 86
50: 86 type=100 (BONDS) 83 84
50: 87 type=100 (BONDS) 83 85
50: 88 type=100 (BONDS) 86 87
50: 89 type=100 (BONDS) 86 88
50: 90 type=105 (BONDS) 89 90
50: 91 type=106 (BONDS) 89 91
50: 92 type=100 (BONDS) 91 92
50: 93 type=107 (BONDS) 91 93
50: 94 type=102 (BONDS) 93 94
50: 95 type=103 (BONDS) 93 95
50: 96 type=104 (BONDS) 93 100
50: 97 type=102 (BONDS) 95 96
50: 98 type=102 (BONDS) 95 97
50: 99 type=113 (BONDS) 95 98
50: 100 type=114 (BONDS) 98 99
50: 101 type=105 (BONDS) 100 101
50: 102 type=106 (BONDS) 100 102
50: 103 type=100 (BONDS) 102 103
50: 104 type=107 (BONDS) 102 104
50: 105 type=102 (BONDS) 104 105
50: 106 type=103 (BONDS) 104 106
50: 107 type=104 (BONDS) 104 115
50: 108 type=102 (BONDS) 106 107
50: 109 type=102 (BONDS) 106 108
50: 110 type=103 (BONDS) 106 109
50: 111 type=102 (BONDS) 109 110
50: 112 type=102 (BONDS) 109 111
50: 113 type=104 (BONDS) 109 112
50: 114 type=115 (BONDS) 112 113
50: 115 type=115 (BONDS) 112 114
50: 116 type=105 (BONDS) 115 116
50: 117 type=106 (BONDS) 115 117
50: 118 type=100 (BONDS) 117 118
50: 119 type=107 (BONDS) 117 119
50: 120 type=102 (BONDS) 119 120
50: 121 type=103 (BONDS) 119 121
50: 122 type=104 (BONDS) 119 134
50: 123 type=102 (BONDS) 121 122
50: 124 type=102 (BONDS) 121 123
50: 125 type=103 (BONDS) 121 124
50: 126 type=102 (BONDS) 124 125
50: 127 type=103 (BONDS) 124 126
50: 128 type=103 (BONDS) 124 130
50: 129 type=102 (BONDS) 126 127
50: 130 type=102 (BONDS) 126 128
50: 131 type=102 (BONDS) 126 129
50: 132 type=102 (BONDS) 130 131
50: 133 type=102 (BONDS) 130 132
50: 134 type=102 (BONDS) 130 133
50: 135 type=105 (BONDS) 134 135
50: 136 type=106 (BONDS) 134 136
50: 137 type=100 (BONDS) 136 137
50: 138 type=107 (BONDS) 136 138
50: 139 type=102 (BONDS) 138 139
50: 140 type=103 (BONDS) 138 140
50: 141 type=104 (BONDS) 138 144
50: 142 type=102 (BONDS) 140 141
50: 143 type=102 (BONDS) 140 142
50: 144 type=102 (BONDS) 140 143
50: 145 type=105 (BONDS) 144 145
50: 146 type=106 (BONDS) 144 146
50: 147 type=100 (BONDS) 146 147
50: 148 type=107 (BONDS) 146 148
50: 149 type=102 (BONDS) 148 149
50: 150 type=103 (BONDS) 148 150
50: 151 type=104 (BONDS) 148 154
50: 152 type=102 (BONDS) 150 151
50: 153 type=102 (BONDS) 150 152
50: 154 type=102 (BONDS) 150 153
50: 155 type=105 (BONDS) 154 155
50: G96Bond:
50: nr: 0
50: Morse:
50: nr: 0
50: Cubic Bonds:
50: nr: 0
50: Connect Bonds:
50: nr: 0
50: Harmonic Pot.:
50: nr: 0
50: FENE Bonds:
50: nr: 0
50: Tab. Bonds:
50: nr: 0
50: Tab. Bonds NC:
50: nr: 0
50: Restraint Pot.:
50: nr: 0
50: Angle:
50: nr: 1124
50: iatoms:
50: 0 type=116 (ANGLES) 1 0 2
50: 1 type=116 (ANGLES) 1 0 3
50: 2 type=116 (ANGLES) 1 0 4
50: 3 type=116 (ANGLES) 2 0 3
50: 4 type=116 (ANGLES) 2 0 4
50: 5 type=116 (ANGLES) 3 0 4
50: 6 type=116 (ANGLES) 0 4 5
50: 7 type=117 (ANGLES) 0 4 6
50: 8 type=117 (ANGLES) 0 4 22
50: 9 type=118 (ANGLES) 5 4 6
50: 10 type=116 (ANGLES) 5 4 22
50: 11 type=119 (ANGLES) 6 4 22
50: 12 type=118 (ANGLES) 4 6 7
50: 13 type=118 (ANGLES) 4 6 8
50: 14 type=120 (ANGLES) 4 6 9
50: 15 type=121 (ANGLES) 7 6 8
50: 16 type=118 (ANGLES) 7 6 9
50: 17 type=118 (ANGLES) 8 6 9
50: 18 type=118 (ANGLES) 6 9 10
50: 19 type=118 (ANGLES) 6 9 11
50: 20 type=120 (ANGLES) 6 9 12
50: 21 type=121 (ANGLES) 10 9 11
50: 22 type=118 (ANGLES) 10 9 12
50: 23 type=118 (ANGLES) 11 9 12
50: 24 type=118 (ANGLES) 9 12 13
50: 25 type=118 (ANGLES) 9 12 14
50: 26 type=120 (ANGLES) 9 12 15
50: 27 type=121 (ANGLES) 13 12 14
50: 28 type=118 (ANGLES) 13 12 15
50: 29 type=118 (ANGLES) 14 12 15
50: 30 type=118 (ANGLES) 12 15 16
50: 31 type=118 (ANGLES) 12 15 17
50: 32 type=117 (ANGLES) 12 15 18
50: 33 type=121 (ANGLES) 16 15 17
50: 34 type=116 (ANGLES) 16 15 18
50: 35 type=116 (ANGLES) 17 15 18
50: 36 type=116 (ANGLES) 15 18 19
50: 37 type=116 (ANGLES) 15 18 20
50: 38 type=116 (ANGLES) 15 18 21
50: 39 type=116 (ANGLES) 19 18 20
50: 40 type=116 (ANGLES) 19 18 21
50: 41 type=116 (ANGLES) 20 18 21
50: 42 type=122 (ANGLES) 4 22 23
50: 43 type=123 (ANGLES) 4 22 24
50: 44 type=124 (ANGLES) 23 22 24
50: 45 type=125 (ANGLES) 22 24 25
50: 46 type=126 (ANGLES) 22 24 26
50: 47 type=127 (ANGLES) 25 24 26
50: 48 type=116 (ANGLES) 24 26 27
50: 49 type=128 (ANGLES) 24 26 28
50: 50 type=129 (ANGLES) 24 26 38
50: 51 type=118 (ANGLES) 27 26 28
50: 52 type=116 (ANGLES) 27 26 38
50: 53 type=119 (ANGLES) 28 26 38
50: 54 type=118 (ANGLES) 26 28 29
50: 55 type=120 (ANGLES) 26 28 30
50: 56 type=120 (ANGLES) 26 28 34
50: 57 type=118 (ANGLES) 29 28 30
50: 58 type=118 (ANGLES) 29 28 34
50: 59 type=120 (ANGLES) 30 28 34
50: 60 type=118 (ANGLES) 28 30 31
50: 61 type=118 (ANGLES) 28 30 32
50: 62 type=118 (ANGLES) 28 30 33
50: 63 type=121 (ANGLES) 31 30 32
50: 64 type=121 (ANGLES) 31 30 33
50: 65 type=121 (ANGLES) 32 30 33
50: 66 type=118 (ANGLES) 28 34 35
50: 67 type=118 (ANGLES) 28 34 36
50: 68 type=118 (ANGLES) 28 34 37
50: 69 type=121 (ANGLES) 35 34 36
50: 70 type=121 (ANGLES) 35 34 37
50: 71 type=121 (ANGLES) 36 34 37
50: 72 type=122 (ANGLES) 26 38 39
50: 73 type=123 (ANGLES) 26 38 40
50: 74 type=124 (ANGLES) 39 38 40
50: 75 type=125 (ANGLES) 38 40 41
50: 76 type=126 (ANGLES) 38 40 42
50: 77 type=127 (ANGLES) 41 40 42
50: 78 type=116 (ANGLES) 40 42 43
50: 79 type=128 (ANGLES) 40 42 44
50: 80 type=129 (ANGLES) 40 42 58
50: 81 type=118 (ANGLES) 43 42 44
50: 82 type=116 (ANGLES) 43 42 58
50: 83 type=119 (ANGLES) 44 42 58
50: 84 type=118 (ANGLES) 42 44 45
50: 85 type=118 (ANGLES) 42 44 46
50: 86 type=130 (ANGLES) 42 44 47
50: 87 type=121 (ANGLES) 45 44 46
50: 88 type=116 (ANGLES) 45 44 47
50: 89 type=116 (ANGLES) 46 44 47
50: 90 type=131 (ANGLES) 44 47 48
50: 91 type=131 (ANGLES) 44 47 50
50: 92 type=132 (ANGLES) 48 47 50
50: 93 type=133 (ANGLES) 47 48 49
50: 94 type=132 (ANGLES) 47 48 52
50: 95 type=133 (ANGLES) 49 48 52
50: 96 type=133 (ANGLES) 47 50 51
50: 97 type=132 (ANGLES) 47 50 54
50: 98 type=133 (ANGLES) 51 50 54
50: 99 type=133 (ANGLES) 48 52 53
50: 100 type=132 (ANGLES) 48 52 56
50: 101 type=133 (ANGLES) 53 52 56
50: 102 type=133 (ANGLES) 50 54 55
50: 103 type=132 (ANGLES) 50 54 56
50: 104 type=133 (ANGLES) 55 54 56
50: 105 type=132 (ANGLES) 52 56 54
50: 106 type=133 (ANGLES) 52 56 57
50: 107 type=133 (ANGLES) 54 56 57
50: 108 type=122 (ANGLES) 42 58 59
50: 109 type=123 (ANGLES) 42 58 60
50: 110 type=124 (ANGLES) 59 58 60
50: 111 type=125 (ANGLES) 58 60 61
50: 112 type=126 (ANGLES) 58 60 62
50: 113 type=127 (ANGLES) 61 60 62
50: 114 type=116 (ANGLES) 60 62 63
50: 115 type=116 (ANGLES) 60 62 64
50: 116 type=129 (ANGLES) 60 62 65
50: 117 type=121 (ANGLES) 63 62 64
50: 118 type=116 (ANGLES) 63 62 65
50: 119 type=116 (ANGLES) 64 62 65
50: 120 type=122 (ANGLES) 62 65 66
50: 121 type=123 (ANGLES) 62 65 67
50: 122 type=124 (ANGLES) 66 65 67
50: 123 type=125 (ANGLES) 65 67 68
50: 124 type=126 (ANGLES) 65 67 69
50: 125 type=127 (ANGLES) 68 67 69
50: 126 type=116 (ANGLES) 67 69 70
50: 127 type=128 (ANGLES) 67 69 71
50: 128 type=129 (ANGLES) 67 69 89
50: 129 type=118 (ANGLES) 70 69 71
50: 130 type=116 (ANGLES) 70 69 89
50: 131 type=119 (ANGLES) 71 69 89
50: 132 type=118 (ANGLES) 69 71 72
50: 133 type=118 (ANGLES) 69 71 73
50: 134 type=120 (ANGLES) 69 71 74
50: 135 type=121 (ANGLES) 72 71 73
50: 136 type=118 (ANGLES) 72 71 74
50: 137 type=118 (ANGLES) 73 71 74
50: 138 type=118 (ANGLES) 71 74 75
50: 139 type=118 (ANGLES) 71 74 76
50: 140 type=120 (ANGLES) 71 74 77
50: 141 type=121 (ANGLES) 75 74 76
50: 142 type=118 (ANGLES) 75 74 77
50: 143 type=118 (ANGLES) 76 74 77
50: 144 type=118 (ANGLES) 74 77 78
50: 145 type=118 (ANGLES) 74 77 79
50: 146 type=117 (ANGLES) 74 77 80
50: 147 type=121 (ANGLES) 78 77 79
50: 148 type=116 (ANGLES) 78 77 80
50: 149 type=116 (ANGLES) 79 77 80
50: 150 type=134 (ANGLES) 77 80 81
50: 151 type=135 (ANGLES) 77 80 82
50: 152 type=133 (ANGLES) 81 80 82
50: 153 type=131 (ANGLES) 80 82 83
50: 154 type=131 (ANGLES) 80 82 86
50: 155 type=131 (ANGLES) 83 82 86
50: 156 type=133 (ANGLES) 82 83 84
50: 157 type=133 (ANGLES) 82 83 85
50: 158 type=133 (ANGLES) 84 83 85
50: 159 type=133 (ANGLES) 82 86 87
50: 160 type=133 (ANGLES) 82 86 88
50: 161 type=133 (ANGLES) 87 86 88
50: 162 type=122 (ANGLES) 69 89 90
50: 163 type=123 (ANGLES) 69 89 91
50: 164 type=124 (ANGLES) 90 89 91
50: 165 type=125 (ANGLES) 89 91 92
50: 166 type=126 (ANGLES) 89 91 93
50: 167 type=127 (ANGLES) 92 91 93
50: 168 type=116 (ANGLES) 91 93 94
50: 169 type=128 (ANGLES) 91 93 95
50: 170 type=129 (ANGLES) 91 93 100
50: 171 type=118 (ANGLES) 94 93 95
50: 172 type=116 (ANGLES) 94 93 100
50: 173 type=119 (ANGLES) 95 93 100
50: 174 type=118 (ANGLES) 93 95 96
50: 175 type=118 (ANGLES) 93 95 97
50: 176 type=136 (ANGLES) 93 95 98
50: 177 type=121 (ANGLES) 96 95 97
50: 178 type=116 (ANGLES) 96 95 98
50: 179 type=116 (ANGLES) 97 95 98
50: 180 type=137 (ANGLES) 95 98 99
50: 181 type=122 (ANGLES) 93 100 101
50: 182 type=123 (ANGLES) 93 100 102
50: 183 type=124 (ANGLES) 101 100 102
50: 184 type=125 (ANGLES) 100 102 103
50: 185 type=126 (ANGLES) 100 102 104
50: 186 type=127 (ANGLES) 103 102 104
50: 187 type=116 (ANGLES) 102 104 105
50: 188 type=128 (ANGLES) 102 104 106
50: 189 type=129 (ANGLES) 102 104 115
50: 190 type=118 (ANGLES) 105 104 106
50: 191 type=116 (ANGLES) 105 104 115
50: 192 type=119 (ANGLES) 106 104 115
50: 193 type=118 (ANGLES) 104 106 107
50: 194 type=118 (ANGLES) 104 106 108
50: 195 type=120 (ANGLES) 104 106 109
50: 196 type=121 (ANGLES) 107 106 108
50: 197 type=118 (ANGLES) 107 106 109
50: 198 type=118 (ANGLES) 108 106 109
50: 199 type=118 (ANGLES) 106 109 110
50: 200 type=118 (ANGLES) 106 109 111
50: 201 type=119 (ANGLES) 106 109 112
50: 202 type=121 (ANGLES) 110 109 111
50: 203 type=116 (ANGLES) 110 109 112
50: 204 type=116 (ANGLES) 111 109 112
50: 205 type=138 (ANGLES) 109 112 113
50: 206 type=138 (ANGLES) 109 112 114
50: 207 type=139 (ANGLES) 113 112 114
50: 208 type=122 (ANGLES) 104 115 116
50: 209 type=123 (ANGLES) 104 115 117
50: 210 type=124 (ANGLES) 116 115 117
50: 211 type=125 (ANGLES) 115 117 118
50: 212 type=126 (ANGLES) 115 117 119
50: 213 type=127 (ANGLES) 118 117 119
50: 214 type=116 (ANGLES) 117 119 120
50: 215 type=128 (ANGLES) 117 119 121
50: 216 type=129 (ANGLES) 117 119 134
50: 217 type=118 (ANGLES) 120 119 121
50: 218 type=116 (ANGLES) 120 119 134
50: 219 type=119 (ANGLES) 121 119 134
50: 220 type=118 (ANGLES) 119 121 122
50: 221 type=118 (ANGLES) 119 121 123
50: 222 type=120 (ANGLES) 119 121 124
50: 223 type=121 (ANGLES) 122 121 123
50: 224 type=118 (ANGLES) 122 121 124
50: 225 type=118 (ANGLES) 123 121 124
50: 226 type=118 (ANGLES) 121 124 125
50: 227 type=120 (ANGLES) 121 124 126
50: 228 type=120 (ANGLES) 121 124 130
50: 229 type=118 (ANGLES) 125 124 126
50: 230 type=118 (ANGLES) 125 124 130
50: 231 type=120 (ANGLES) 126 124 130
50: 232 type=118 (ANGLES) 124 126 127
50: 233 type=118 (ANGLES) 124 126 128
50: 234 type=118 (ANGLES) 124 126 129
50: 235 type=121 (ANGLES) 127 126 128
50: 236 type=121 (ANGLES) 127 126 129
50: 237 type=121 (ANGLES) 128 126 129
50: 238 type=118 (ANGLES) 124 130 131
50: 239 type=118 (ANGLES) 124 130 132
50: 240 type=118 (ANGLES) 124 130 133
50: 241 type=121 (ANGLES) 131 130 132
50: 242 type=121 (ANGLES) 131 130 133
50: 243 type=121 (ANGLES) 132 130 133
50: 244 type=122 (ANGLES) 119 134 135
50: 245 type=123 (ANGLES) 119 134 136
50: 246 type=124 (ANGLES) 135 134 136
50: 247 type=125 (ANGLES) 134 136 137
50: 248 type=126 (ANGLES) 134 136 138
50: 249 type=127 (ANGLES) 137 136 138
50: 250 type=116 (ANGLES) 136 138 139
50: 251 type=128 (ANGLES) 136 138 140
50: 252 type=129 (ANGLES) 136 138 144
50: 253 type=118 (ANGLES) 139 138 140
50: 254 type=116 (ANGLES) 139 138 144
50: 255 type=119 (ANGLES) 140 138 144
50: 256 type=118 (ANGLES) 138 140 141
50: 257 type=118 (ANGLES) 138 140 142
50: 258 type=118 (ANGLES) 138 140 143
50: 259 type=121 (ANGLES) 141 140 142
50: 260 type=121 (ANGLES) 141 140 143
50: 261 type=121 (ANGLES) 142 140 143
50: 262 type=122 (ANGLES) 138 144 145
50: 263 type=123 (ANGLES) 138 144 146
50: 264 type=124 (ANGLES) 145 144 146
50: 265 type=125 (ANGLES) 144 146 147
50: 266 type=126 (ANGLES) 144 146 148
50: 267 type=127 (ANGLES) 147 146 148
50: 268 type=116 (ANGLES) 146 148 149
50: 269 type=128 (ANGLES) 146 148 150
50: 270 type=129 (ANGLES) 146 148 154
50: 271 type=118 (ANGLES) 149 148 150
50: 272 type=116 (ANGLES) 149 148 154
50: 273 type=119 (ANGLES) 150 148 154
50: 274 type=118 (ANGLES) 148 150 151
50: 275 type=118 (ANGLES) 148 150 152
50: 276 type=118 (ANGLES) 148 150 153
50: 277 type=121 (ANGLES) 151 150 152
50: 278 type=121 (ANGLES) 151 150 153
50: 279 type=121 (ANGLES) 152 150 153
50: 280 type=122 (ANGLES) 148 154 155
50: G96Angle:
50: nr: 0
50: Restricted Angles:
50: nr: 0
50: Lin. Angle:
50: nr: 0
50: Bond-Cross:
50: nr: 0
50: BA-Cross:
50: nr: 0
50: U-B:
50: nr: 0
50: Quartic Angles:
50: nr: 0
50: Tab. Angles:
50: nr: 0
50: Proper Dih.:
50: nr: 145
50: iatoms:
50: 0 type=140 (PDIHS) 4 24 22 23
50: 1 type=141 (PDIHS) 22 26 24 25
50: 2 type=140 (PDIHS) 26 40 38 39
50: 3 type=141 (PDIHS) 38 42 40 41
50: 4 type=140 (PDIHS) 42 60 58 59
50: 5 type=142 (PDIHS) 44 47 50 48
50: 6 type=142 (PDIHS) 47 52 48 49
50: 7 type=142 (PDIHS) 47 54 50 51
50: 8 type=142 (PDIHS) 48 56 52 53
50: 9 type=142 (PDIHS) 50 56 54 55
50: 10 type=142 (PDIHS) 52 54 56 57
50: 11 type=141 (PDIHS) 58 62 60 61
50: 12 type=140 (PDIHS) 62 67 65 66
50: 13 type=141 (PDIHS) 65 69 67 68
50: 14 type=140 (PDIHS) 69 91 89 90
50: 15 type=141 (PDIHS) 77 82 80 81
50: 16 type=140 (PDIHS) 80 83 82 86
50: 17 type=141 (PDIHS) 82 84 83 85
50: 18 type=141 (PDIHS) 82 87 86 88
50: 19 type=141 (PDIHS) 89 93 91 92
50: 20 type=140 (PDIHS) 93 102 100 101
50: 21 type=141 (PDIHS) 100 104 102 103
50: 22 type=140 (PDIHS) 104 117 115 116
50: 23 type=140 (PDIHS) 109 113 112 114
50: 24 type=141 (PDIHS) 115 119 117 118
50: 25 type=140 (PDIHS) 119 136 134 135
50: 26 type=141 (PDIHS) 134 138 136 137
50: 27 type=140 (PDIHS) 138 146 144 145
50: 28 type=141 (PDIHS) 144 148 146 147
50: Ryckaert-Bell.:
50: nr: 1565
50: iatoms:
50: 0 type=143 (RBDIHS) 1 0 4 5
50: 1 type=144 (RBDIHS) 1 0 4 6
50: 2 type=144 (RBDIHS) 1 0 4 22
50: 3 type=143 (RBDIHS) 2 0 4 5
50: 4 type=144 (RBDIHS) 2 0 4 6
50: 5 type=144 (RBDIHS) 2 0 4 22
50: 6 type=143 (RBDIHS) 3 0 4 5
50: 7 type=144 (RBDIHS) 3 0 4 6
50: 8 type=144 (RBDIHS) 3 0 4 22
50: 9 type=145 (RBDIHS) 0 4 6 9
50: 10 type=146 (RBDIHS) 22 4 6 9
50: 11 type=147 (RBDIHS) 0 4 6 7
50: 12 type=147 (RBDIHS) 0 4 6 8
50: 13 type=148 (RBDIHS) 5 4 6 7
50: 14 type=148 (RBDIHS) 5 4 6 8
50: 15 type=148 (RBDIHS) 5 4 6 9
50: 16 type=149 (RBDIHS) 22 4 6 7
50: 17 type=149 (RBDIHS) 22 4 6 8
50: 18 type=150 (RBDIHS) 0 4 22 24
50: 19 type=151 (RBDIHS) 6 4 22 24
50: 20 type=148 (RBDIHS) 4 6 9 10
50: 21 type=148 (RBDIHS) 4 6 9 11
50: 22 type=152 (RBDIHS) 4 6 9 12
50: 23 type=148 (RBDIHS) 7 6 9 10
50: 24 type=148 (RBDIHS) 7 6 9 11
50: 25 type=148 (RBDIHS) 7 6 9 12
50: 26 type=148 (RBDIHS) 8 6 9 10
50: 27 type=148 (RBDIHS) 8 6 9 11
50: 28 type=148 (RBDIHS) 8 6 9 12
50: 29 type=148 (RBDIHS) 6 9 12 13
50: 30 type=148 (RBDIHS) 6 9 12 14
50: 31 type=152 (RBDIHS) 6 9 12 15
50: 32 type=148 (RBDIHS) 10 9 12 13
50: 33 type=148 (RBDIHS) 10 9 12 14
50: 34 type=148 (RBDIHS) 10 9 12 15
50: 35 type=148 (RBDIHS) 11 9 12 13
50: 36 type=148 (RBDIHS) 11 9 12 14
50: 37 type=148 (RBDIHS) 11 9 12 15
50: 38 type=148 (RBDIHS) 9 12 15 16
50: 39 type=148 (RBDIHS) 9 12 15 17
50: 40 type=153 (RBDIHS) 9 12 15 18
50: 41 type=148 (RBDIHS) 13 12 15 16
50: 42 type=148 (RBDIHS) 13 12 15 17
50: 43 type=154 (RBDIHS) 13 12 15 18
50: 44 type=148 (RBDIHS) 14 12 15 16
50: 45 type=148 (RBDIHS) 14 12 15 17
50: 46 type=154 (RBDIHS) 14 12 15 18
50: 47 type=144 (RBDIHS) 12 15 18 19
50: 48 type=144 (RBDIHS) 12 15 18 20
50: 49 type=144 (RBDIHS) 12 15 18 21
50: 50 type=143 (RBDIHS) 16 15 18 19
50: 51 type=143 (RBDIHS) 16 15 18 20
50: 52 type=143 (RBDIHS) 16 15 18 21
50: 53 type=143 (RBDIHS) 17 15 18 19
50: 54 type=143 (RBDIHS) 17 15 18 20
50: 55 type=143 (RBDIHS) 17 15 18 21
50: 56 type=155 (RBDIHS) 4 22 24 25
50: 57 type=156 (RBDIHS) 4 22 24 26
50: 58 type=155 (RBDIHS) 23 22 24 25
50: 59 type=157 (RBDIHS) 23 22 24 26
50: 60 type=158 (RBDIHS) 22 24 26 28
50: 61 type=159 (RBDIHS) 22 24 26 38
50: 62 type=160 (RBDIHS) 24 26 28 30
50: 63 type=160 (RBDIHS) 24 26 28 34
50: 64 type=161 (RBDIHS) 38 26 28 30
50: 65 type=161 (RBDIHS) 38 26 28 34
50: 66 type=147 (RBDIHS) 24 26 28 29
50: 67 type=148 (RBDIHS) 27 26 28 29
50: 68 type=148 (RBDIHS) 27 26 28 30
50: 69 type=148 (RBDIHS) 27 26 28 34
50: 70 type=149 (RBDIHS) 38 26 28 29
50: 71 type=150 (RBDIHS) 24 26 38 40
50: 72 type=151 (RBDIHS) 28 26 38 40
50: 73 type=148 (RBDIHS) 26 28 30 31
50: 74 type=148 (RBDIHS) 26 28 30 32
50: 75 type=148 (RBDIHS) 26 28 30 33
50: 76 type=148 (RBDIHS) 29 28 30 31
50: 77 type=148 (RBDIHS) 29 28 30 32
50: 78 type=148 (RBDIHS) 29 28 30 33
50: 79 type=148 (RBDIHS) 34 28 30 31
50: 80 type=148 (RBDIHS) 34 28 30 32
50: 81 type=148 (RBDIHS) 34 28 30 33
50: 82 type=148 (RBDIHS) 26 28 34 35
50: 83 type=148 (RBDIHS) 26 28 34 36
50: 84 type=148 (RBDIHS) 26 28 34 37
50: 85 type=148 (RBDIHS) 29 28 34 35
50: 86 type=148 (RBDIHS) 29 28 34 36
50: 87 type=148 (RBDIHS) 29 28 34 37
50: 88 type=148 (RBDIHS) 30 28 34 35
50: 89 type=148 (RBDIHS) 30 28 34 36
50: 90 type=148 (RBDIHS) 30 28 34 37
50: 91 type=155 (RBDIHS) 26 38 40 41
50: 92 type=156 (RBDIHS) 26 38 40 42
50: 93 type=155 (RBDIHS) 39 38 40 41
50: 94 type=157 (RBDIHS) 39 38 40 42
50: 95 type=158 (RBDIHS) 38 40 42 44
50: 96 type=159 (RBDIHS) 38 40 42 58
50: 97 type=147 (RBDIHS) 40 42 44 45
50: 98 type=147 (RBDIHS) 40 42 44 46
50: 99 type=162 (RBDIHS) 40 42 44 47
50: 100 type=148 (RBDIHS) 43 42 44 45
50: 101 type=148 (RBDIHS) 43 42 44 46
50: 102 type=163 (RBDIHS) 43 42 44 47
50: 103 type=149 (RBDIHS) 58 42 44 45
50: 104 type=149 (RBDIHS) 58 42 44 46
50: 105 type=164 (RBDIHS) 58 42 44 47
50: 106 type=150 (RBDIHS) 40 42 58 60
50: 107 type=151 (RBDIHS) 44 42 58 60
50: 108 type=165 (RBDIHS) 44 47 48 49
50: 109 type=165 (RBDIHS) 44 47 48 52
50: 110 type=165 (RBDIHS) 50 47 48 49
50: 111 type=165 (RBDIHS) 50 47 48 52
50: 112 type=165 (RBDIHS) 44 47 50 51
50: 113 type=165 (RBDIHS) 44 47 50 54
50: 114 type=165 (RBDIHS) 48 47 50 51
50: 115 type=165 (RBDIHS) 48 47 50 54
50: 116 type=165 (RBDIHS) 47 48 52 53
50: 117 type=165 (RBDIHS) 47 48 52 56
50: 118 type=165 (RBDIHS) 49 48 52 53
50: 119 type=165 (RBDIHS) 49 48 52 56
50: 120 type=165 (RBDIHS) 47 50 54 55
50: 121 type=165 (RBDIHS) 47 50 54 56
50: 122 type=165 (RBDIHS) 51 50 54 55
50: 123 type=165 (RBDIHS) 51 50 54 56
50: 124 type=165 (RBDIHS) 48 52 56 54
50: 125 type=165 (RBDIHS) 48 52 56 57
50: 126 type=165 (RBDIHS) 53 52 56 54
50: 127 type=165 (RBDIHS) 53 52 56 57
50: 128 type=165 (RBDIHS) 50 54 56 52
50: 129 type=165 (RBDIHS) 50 54 56 57
50: 130 type=165 (RBDIHS) 55 54 56 52
50: 131 type=165 (RBDIHS) 55 54 56 57
50: 132 type=155 (RBDIHS) 42 58 60 61
50: 133 type=156 (RBDIHS) 42 58 60 62
50: 134 type=155 (RBDIHS) 59 58 60 61
50: 135 type=157 (RBDIHS) 59 58 60 62
50: 136 type=159 (RBDIHS) 58 60 62 65
50: 137 type=150 (RBDIHS) 60 62 65 67
50: 138 type=155 (RBDIHS) 62 65 67 68
50: 139 type=156 (RBDIHS) 62 65 67 69
50: 140 type=155 (RBDIHS) 66 65 67 68
50: 141 type=157 (RBDIHS) 66 65 67 69
50: 142 type=158 (RBDIHS) 65 67 69 71
50: 143 type=159 (RBDIHS) 65 67 69 89
50: 144 type=166 (RBDIHS) 67 69 71 74
50: 145 type=167 (RBDIHS) 89 69 71 74
50: 146 type=147 (RBDIHS) 67 69 71 72
50: 147 type=147 (RBDIHS) 67 69 71 73
50: 148 type=148 (RBDIHS) 70 69 71 72
50: 149 type=148 (RBDIHS) 70 69 71 73
50: 150 type=148 (RBDIHS) 70 69 71 74
50: 151 type=149 (RBDIHS) 89 69 71 72
50: 152 type=149 (RBDIHS) 89 69 71 73
50: 153 type=150 (RBDIHS) 67 69 89 91
50: 154 type=151 (RBDIHS) 71 69 89 91
50: 155 type=148 (RBDIHS) 69 71 74 75
50: 156 type=148 (RBDIHS) 69 71 74 76
50: 157 type=152 (RBDIHS) 69 71 74 77
50: 158 type=148 (RBDIHS) 72 71 74 75
50: 159 type=148 (RBDIHS) 72 71 74 76
50: 160 type=148 (RBDIHS) 72 71 74 77
50: 161 type=148 (RBDIHS) 73 71 74 75
50: 162 type=148 (RBDIHS) 73 71 74 76
50: 163 type=148 (RBDIHS) 73 71 74 77
50: 164 type=148 (RBDIHS) 71 74 77 78
50: 165 type=148 (RBDIHS) 71 74 77 79
50: 166 type=153 (RBDIHS) 71 74 77 80
50: 167 type=148 (RBDIHS) 75 74 77 78
50: 168 type=148 (RBDIHS) 75 74 77 79
50: 169 type=168 (RBDIHS) 75 74 77 80
50: 170 type=148 (RBDIHS) 76 74 77 78
50: 171 type=148 (RBDIHS) 76 74 77 79
50: 172 type=168 (RBDIHS) 76 74 77 80
50: 173 type=169 (RBDIHS) 74 77 80 81
50: 174 type=170 (RBDIHS) 74 77 80 82
50: 175 type=171 (RBDIHS) 78 77 80 82
50: 176 type=171 (RBDIHS) 79 77 80 82
50: 177 type=172 (RBDIHS) 77 80 82 83
50: 178 type=172 (RBDIHS) 77 80 82 86
50: 179 type=173 (RBDIHS) 81 80 82 83
50: 180 type=173 (RBDIHS) 81 80 82 86
50: 181 type=173 (RBDIHS) 80 82 83 84
50: 182 type=173 (RBDIHS) 80 82 83 85
50: 183 type=173 (RBDIHS) 86 82 83 84
50: 184 type=173 (RBDIHS) 86 82 83 85
50: 185 type=173 (RBDIHS) 80 82 86 87
50: 186 type=173 (RBDIHS) 80 82 86 88
50: 187 type=173 (RBDIHS) 83 82 86 87
50: 188 type=173 (RBDIHS) 83 82 86 88
50: 189 type=155 (RBDIHS) 69 89 91 92
50: 190 type=156 (RBDIHS) 69 89 91 93
50: 191 type=155 (RBDIHS) 90 89 91 92
50: 192 type=157 (RBDIHS) 90 89 91 93
50: 193 type=158 (RBDIHS) 89 91 93 95
50: 194 type=159 (RBDIHS) 89 91 93 100
50: 195 type=174 (RBDIHS) 91 93 95 98
50: 196 type=175 (RBDIHS) 100 93 95 98
50: 197 type=147 (RBDIHS) 91 93 95 96
50: 198 type=147 (RBDIHS) 91 93 95 97
50: 199 type=148 (RBDIHS) 94 93 95 96
50: 200 type=148 (RBDIHS) 94 93 95 97
50: 201 type=176 (RBDIHS) 94 93 95 98
50: 202 type=149 (RBDIHS) 100 93 95 96
50: 203 type=149 (RBDIHS) 100 93 95 97
50: 204 type=150 (RBDIHS) 91 93 100 102
50: 205 type=151 (RBDIHS) 95 93 100 102
50: 206 type=177 (RBDIHS) 93 95 98 99
50: 207 type=178 (RBDIHS) 96 95 98 99
50: 208 type=178 (RBDIHS) 97 95 98 99
50: 209 type=155 (RBDIHS) 93 100 102 103
50: 210 type=156 (RBDIHS) 93 100 102 104
50: 211 type=155 (RBDIHS) 101 100 102 103
50: 212 type=157 (RBDIHS) 101 100 102 104
50: 213 type=158 (RBDIHS) 100 102 104 106
50: 214 type=159 (RBDIHS) 100 102 104 115
50: 215 type=179 (RBDIHS) 102 104 106 109
50: 216 type=180 (RBDIHS) 115 104 106 109
50: 217 type=147 (RBDIHS) 102 104 106 107
50: 218 type=147 (RBDIHS) 102 104 106 108
50: 219 type=148 (RBDIHS) 105 104 106 107
50: 220 type=148 (RBDIHS) 105 104 106 108
50: 221 type=148 (RBDIHS) 105 104 106 109
50: 222 type=149 (RBDIHS) 115 104 106 107
50: 223 type=149 (RBDIHS) 115 104 106 108
50: 224 type=150 (RBDIHS) 102 104 115 117
50: 225 type=151 (RBDIHS) 106 104 115 117
50: 226 type=148 (RBDIHS) 104 106 109 110
50: 227 type=148 (RBDIHS) 104 106 109 111
50: 228 type=181 (RBDIHS) 104 106 109 112
50: 229 type=148 (RBDIHS) 107 106 109 110
50: 230 type=148 (RBDIHS) 107 106 109 111
50: 231 type=182 (RBDIHS) 107 106 109 112
50: 232 type=148 (RBDIHS) 108 106 109 110
50: 233 type=148 (RBDIHS) 108 106 109 111
50: 234 type=182 (RBDIHS) 108 106 109 112
50: 235 type=183 (RBDIHS) 106 109 112 113
50: 236 type=183 (RBDIHS) 106 109 112 114
50: 237 type=155 (RBDIHS) 104 115 117 118
50: 238 type=156 (RBDIHS) 104 115 117 119
50: 239 type=155 (RBDIHS) 116 115 117 118
50: 240 type=157 (RBDIHS) 116 115 117 119
50: 241 type=158 (RBDIHS) 115 117 119 121
50: 242 type=159 (RBDIHS) 115 117 119 134
50: 243 type=184 (RBDIHS) 117 119 121 124
50: 244 type=185 (RBDIHS) 134 119 121 124
50: 245 type=147 (RBDIHS) 117 119 121 122
50: 246 type=147 (RBDIHS) 117 119 121 123
50: 247 type=148 (RBDIHS) 120 119 121 122
50: 248 type=148 (RBDIHS) 120 119 121 123
50: 249 type=148 (RBDIHS) 120 119 121 124
50: 250 type=149 (RBDIHS) 134 119 121 122
50: 251 type=149 (RBDIHS) 134 119 121 123
50: 252 type=150 (RBDIHS) 117 119 134 136
50: 253 type=151 (RBDIHS) 121 119 134 136
50: 254 type=148 (RBDIHS) 119 121 124 125
50: 255 type=152 (RBDIHS) 119 121 124 126
50: 256 type=152 (RBDIHS) 119 121 124 130
50: 257 type=148 (RBDIHS) 122 121 124 125
50: 258 type=148 (RBDIHS) 122 121 124 126
50: 259 type=148 (RBDIHS) 122 121 124 130
50: 260 type=148 (RBDIHS) 123 121 124 125
50: 261 type=148 (RBDIHS) 123 121 124 126
50: 262 type=148 (RBDIHS) 123 121 124 130
50: 263 type=148 (RBDIHS) 121 124 126 127
50: 264 type=148 (RBDIHS) 121 124 126 128
50: 265 type=148 (RBDIHS) 121 124 126 129
50: 266 type=148 (RBDIHS) 125 124 126 127
50: 267 type=148 (RBDIHS) 125 124 126 128
50: 268 type=148 (RBDIHS) 125 124 126 129
50: 269 type=148 (RBDIHS) 130 124 126 127
50: 270 type=148 (RBDIHS) 130 124 126 128
50: 271 type=148 (RBDIHS) 130 124 126 129
50: 272 type=148 (RBDIHS) 121 124 130 131
50: 273 type=148 (RBDIHS) 121 124 130 132
50: 274 type=148 (RBDIHS) 121 124 130 133
50: 275 type=148 (RBDIHS) 125 124 130 131
50: 276 type=148 (RBDIHS) 125 124 130 132
50: 277 type=148 (RBDIHS) 125 124 130 133
50: 278 type=148 (RBDIHS) 126 124 130 131
50: 279 type=148 (RBDIHS) 126 124 130 132
50: 280 type=148 (RBDIHS) 126 124 130 133
50: 281 type=155 (RBDIHS) 119 134 136 137
50: 282 type=156 (RBDIHS) 119 134 136 138
50: 283 type=155 (RBDIHS) 135 134 136 137
50: 284 type=157 (RBDIHS) 135 134 136 138
50: 285 type=158 (RBDIHS) 134 136 138 140
50: 286 type=159 (RBDIHS) 134 136 138 144
50: 287 type=147 (RBDIHS) 136 138 140 141
50: 288 type=147 (RBDIHS) 136 138 140 142
50: 289 type=147 (RBDIHS) 136 138 140 143
50: 290 type=148 (RBDIHS) 139 138 140 141
50: 291 type=148 (RBDIHS) 139 138 140 142
50: 292 type=148 (RBDIHS) 139 138 140 143
50: 293 type=149 (RBDIHS) 144 138 140 141
50: 294 type=149 (RBDIHS) 144 138 140 142
50: 295 type=149 (RBDIHS) 144 138 140 143
50: 296 type=150 (RBDIHS) 136 138 144 146
50: 297 type=151 (RBDIHS) 140 138 144 146
50: 298 type=155 (RBDIHS) 138 144 146 147
50: 299 type=156 (RBDIHS) 138 144 146 148
50: 300 type=155 (RBDIHS) 145 144 146 147
50: 301 type=157 (RBDIHS) 145 144 146 148
50: 302 type=158 (RBDIHS) 144 146 148 150
50: 303 type=159 (RBDIHS) 144 146 148 154
50: 304 type=147 (RBDIHS) 146 148 150 151
50: 305 type=147 (RBDIHS) 146 148 150 152
50: 306 type=147 (RBDIHS) 146 148 150 153
50: 307 type=148 (RBDIHS) 149 148 150 151
50: 308 type=148 (RBDIHS) 149 148 150 152
50: 309 type=148 (RBDIHS) 149 148 150 153
50: 310 type=149 (RBDIHS) 154 148 150 151
50: 311 type=149 (RBDIHS) 154 148 150 152
50: 312 type=149 (RBDIHS) 154 148 150 153
50: Restricted Dih.:
50: nr: 0
50: CBT Dih.:
50: nr: 0
50: Fourier Dih.:
50: nr: 0
50: Improper Dih.:
50: nr: 0
50: Improper Dih.:
50: nr: 0
50: Tab. Dih.:
50: nr: 0
50: CMAP Dih.:
50: nr: 0
50: GB 1-2 Pol. (unused):
50: nr: 0
50: GB 1-3 Pol. (unused):
50: nr: 0
50: GB 1-4 Pol. (unused):
50: nr: 0
50: GB Polarization (unused):
50: nr: 0
50: Nonpolar Sol. (unused):
50: nr: 0
50: LJ-14:
50: nr: 1197
50: iatoms:
50: 0 type=186 (LJ14) 0 7
50: 1 type=186 (LJ14) 0 8
50: 2 type=187 (LJ14) 0 9
50: 3 type=188 (LJ14) 0 23
50: 4 type=189 (LJ14) 0 24
50: 5 type=190 (LJ14) 1 5
50: 6 type=190 (LJ14) 1 6
50: 7 type=190 (LJ14) 1 22
50: 8 type=190 (LJ14) 2 5
50: 9 type=190 (LJ14) 2 6
50: 10 type=190 (LJ14) 2 22
50: 11 type=190 (LJ14) 3 5
50: 12 type=190 (LJ14) 3 6
50: 13 type=190 (LJ14) 3 22
50: 14 type=191 (LJ14) 4 10
50: 15 type=191 (LJ14) 4 11
50: 16 type=192 (LJ14) 4 12
50: 17 type=190 (LJ14) 4 25
50: 18 type=192 (LJ14) 4 26
50: 19 type=193 (LJ14) 5 7
50: 20 type=193 (LJ14) 5 8
50: 21 type=191 (LJ14) 5 9
50: 22 type=194 (LJ14) 5 23
50: 23 type=186 (LJ14) 5 24
50: 24 type=191 (LJ14) 6 13
50: 25 type=191 (LJ14) 6 14
50: 26 type=192 (LJ14) 6 15
50: 27 type=195 (LJ14) 6 23
50: 28 type=187 (LJ14) 6 24
50: 29 type=193 (LJ14) 7 10
50: 30 type=193 (LJ14) 7 11
50: 31 type=191 (LJ14) 7 12
50: 32 type=196 (LJ14) 7 22
50: 33 type=193 (LJ14) 8 10
50: 34 type=193 (LJ14) 8 11
50: 35 type=191 (LJ14) 8 12
50: 36 type=196 (LJ14) 8 22
50: 37 type=191 (LJ14) 9 16
50: 38 type=191 (LJ14) 9 17
50: 39 type=187 (LJ14) 9 18
50: 40 type=197 (LJ14) 9 22
50: 41 type=193 (LJ14) 10 13
50: 42 type=193 (LJ14) 10 14
50: 43 type=191 (LJ14) 10 15
50: 44 type=193 (LJ14) 11 13
50: 45 type=193 (LJ14) 11 14
50: 46 type=191 (LJ14) 11 15
50: 47 type=190 (LJ14) 12 19
50: 48 type=190 (LJ14) 12 20
50: 49 type=190 (LJ14) 12 21
50: 50 type=193 (LJ14) 13 16
50: 51 type=193 (LJ14) 13 17
50: 52 type=186 (LJ14) 13 18
50: 53 type=193 (LJ14) 14 16
50: 54 type=193 (LJ14) 14 17
50: 55 type=186 (LJ14) 14 18
50: 56 type=190 (LJ14) 16 19
50: 57 type=190 (LJ14) 16 20
50: 58 type=190 (LJ14) 16 21
50: 59 type=190 (LJ14) 17 19
50: 60 type=190 (LJ14) 17 20
50: 61 type=190 (LJ14) 17 21
50: 62 type=196 (LJ14) 22 27
50: 63 type=197 (LJ14) 22 28
50: 64 type=198 (LJ14) 22 38
50: 65 type=190 (LJ14) 23 25
50: 66 type=195 (LJ14) 23 26
50: 67 type=186 (LJ14) 24 29
50: 68 type=187 (LJ14) 24 30
50: 69 type=187 (LJ14) 24 34
50: 70 type=188 (LJ14) 24 39
50: 71 type=189 (LJ14) 24 40
50: 72 type=190 (LJ14) 25 27
50: 73 type=190 (LJ14) 25 28
50: 74 type=190 (LJ14) 25 38
50: 75 type=191 (LJ14) 26 31
50: 76 type=191 (LJ14) 26 32
50: 77 type=191 (LJ14) 26 33
50: 78 type=191 (LJ14) 26 35
50: 79 type=191 (LJ14) 26 36
50: 80 type=191 (LJ14) 26 37
50: 81 type=190 (LJ14) 26 41
50: 82 type=192 (LJ14) 26 42
50: 83 type=193 (LJ14) 27 29
50: 84 type=191 (LJ14) 27 30
50: 85 type=191 (LJ14) 27 34
50: 86 type=194 (LJ14) 27 39
50: 87 type=186 (LJ14) 27 40
50: 88 type=195 (LJ14) 28 39
50: 89 type=187 (LJ14) 28 40
50: 90 type=193 (LJ14) 29 31
50: 91 type=193 (LJ14) 29 32
50: 92 type=193 (LJ14) 29 33
50: 93 type=193 (LJ14) 29 35
50: 94 type=193 (LJ14) 29 36
50: 95 type=193 (LJ14) 29 37
50: 96 type=196 (LJ14) 29 38
50: 97 type=191 (LJ14) 30 35
50: 98 type=191 (LJ14) 30 36
50: 99 type=191 (LJ14) 30 37
50: 100 type=197 (LJ14) 30 38
50: 101 type=191 (LJ14) 31 34
50: 102 type=191 (LJ14) 32 34
50: 103 type=191 (LJ14) 33 34
50: 104 type=197 (LJ14) 34 38
50: 105 type=196 (LJ14) 38 43
50: 106 type=197 (LJ14) 38 44
50: 107 type=198 (LJ14) 38 58
50: 108 type=190 (LJ14) 39 41
50: 109 type=195 (LJ14) 39 42
50: 110 type=186 (LJ14) 40 45
50: 111 type=186 (LJ14) 40 46
50: 112 type=199 (LJ14) 40 47
50: 113 type=188 (LJ14) 40 59
50: 114 type=189 (LJ14) 40 60
50: 115 type=190 (LJ14) 41 43
50: 116 type=190 (LJ14) 41 44
50: 117 type=190 (LJ14) 41 58
50: 118 type=200 (LJ14) 42 48
50: 119 type=200 (LJ14) 42 50
50: 120 type=190 (LJ14) 42 61
50: 121 type=192 (LJ14) 42 62
50: 122 type=193 (LJ14) 43 45
50: 123 type=193 (LJ14) 43 46
50: 124 type=201 (LJ14) 43 47
50: 125 type=194 (LJ14) 43 59
50: 126 type=186 (LJ14) 43 60
50: 127 type=202 (LJ14) 44 49
50: 128 type=202 (LJ14) 44 51
50: 129 type=200 (LJ14) 44 52
50: 130 type=200 (LJ14) 44 54
50: 131 type=195 (LJ14) 44 59
50: 132 type=187 (LJ14) 44 60
50: 133 type=201 (LJ14) 45 48
50: 134 type=201 (LJ14) 45 50
50: 135 type=196 (LJ14) 45 58
50: 136 type=201 (LJ14) 46 48
50: 137 type=201 (LJ14) 46 50
50: 138 type=196 (LJ14) 46 58
50: 139 type=203 (LJ14) 47 53
50: 140 type=203 (LJ14) 47 55
50: 141 type=204 (LJ14) 47 56
50: 142 type=205 (LJ14) 47 58
50: 143 type=203 (LJ14) 48 51
50: 144 type=204 (LJ14) 48 54
50: 145 type=203 (LJ14) 48 57
50: 146 type=203 (LJ14) 49 50
50: 147 type=206 (LJ14) 49 53
50: 148 type=203 (LJ14) 49 56
50: 149 type=204 (LJ14) 50 52
50: 150 type=203 (LJ14) 50 57
50: 151 type=206 (LJ14) 51 55
50: 152 type=203 (LJ14) 51 56
50: 153 type=203 (LJ14) 52 55
50: 154 type=203 (LJ14) 53 54
50: 155 type=206 (LJ14) 53 57
50: 156 type=206 (LJ14) 55 57
50: 157 type=196 (LJ14) 58 63
50: 158 type=196 (LJ14) 58 64
50: 159 type=198 (LJ14) 58 65
50: 160 type=190 (LJ14) 59 61
50: 161 type=195 (LJ14) 59 62
50: 162 type=188 (LJ14) 60 66
50: 163 type=189 (LJ14) 60 67
50: 164 type=190 (LJ14) 61 63
50: 165 type=190 (LJ14) 61 64
50: 166 type=190 (LJ14) 61 65
50: 167 type=190 (LJ14) 62 68
50: 168 type=192 (LJ14) 62 69
50: 169 type=194 (LJ14) 63 66
50: 170 type=186 (LJ14) 63 67
50: 171 type=194 (LJ14) 64 66
50: 172 type=186 (LJ14) 64 67
50: 173 type=196 (LJ14) 65 70
50: 174 type=197 (LJ14) 65 71
50: 175 type=198 (LJ14) 65 89
50: 176 type=190 (LJ14) 66 68
50: 177 type=195 (LJ14) 66 69
50: 178 type=186 (LJ14) 67 72
50: 179 type=186 (LJ14) 67 73
50: 180 type=187 (LJ14) 67 74
50: 181 type=188 (LJ14) 67 90
50: 182 type=189 (LJ14) 67 91
50: 183 type=190 (LJ14) 68 70
50: 184 type=190 (LJ14) 68 71
50: 185 type=190 (LJ14) 68 89
50: 186 type=191 (LJ14) 69 75
50: 187 type=191 (LJ14) 69 76
50: 188 type=192 (LJ14) 69 77
50: 189 type=190 (LJ14) 69 92
50: 190 type=192 (LJ14) 69 93
50: 191 type=193 (LJ14) 70 72
50: 192 type=193 (LJ14) 70 73
50: 193 type=191 (LJ14) 70 74
50: 194 type=194 (LJ14) 70 90
50: 195 type=186 (LJ14) 70 91
50: 196 type=191 (LJ14) 71 78
50: 197 type=191 (LJ14) 71 79
50: 198 type=187 (LJ14) 71 80
50: 199 type=195 (LJ14) 71 90
50: 200 type=187 (LJ14) 71 91
50: 201 type=193 (LJ14) 72 75
50: 202 type=193 (LJ14) 72 76
50: 203 type=191 (LJ14) 72 77
50: 204 type=196 (LJ14) 72 89
50: 205 type=193 (LJ14) 73 75
50: 206 type=193 (LJ14) 73 76
50: 207 type=191 (LJ14) 73 77
50: 208 type=196 (LJ14) 73 89
50: 209 type=190 (LJ14) 74 81
50: 210 type=207 (LJ14) 74 82
50: 211 type=197 (LJ14) 74 89
50: 212 type=193 (LJ14) 75 78
50: 213 type=193 (LJ14) 75 79
50: 214 type=186 (LJ14) 75 80
50: 215 type=193 (LJ14) 76 78
50: 216 type=193 (LJ14) 76 79
50: 217 type=186 (LJ14) 76 80
50: 218 type=187 (LJ14) 77 83
50: 219 type=187 (LJ14) 77 86
50: 220 type=190 (LJ14) 78 81
50: 221 type=208 (LJ14) 78 82
50: 222 type=190 (LJ14) 79 81
50: 223 type=208 (LJ14) 79 82
50: 224 type=190 (LJ14) 80 84
50: 225 type=190 (LJ14) 80 85
50: 226 type=190 (LJ14) 80 87
50: 227 type=190 (LJ14) 80 88
50: 228 type=190 (LJ14) 81 83
50: 229 type=190 (LJ14) 81 86
50: 230 type=190 (LJ14) 83 87
50: 231 type=190 (LJ14) 83 88
50: 232 type=190 (LJ14) 84 86
50: 233 type=190 (LJ14) 85 86
50: 234 type=196 (LJ14) 89 94
50: 235 type=197 (LJ14) 89 95
50: 236 type=198 (LJ14) 89 100
50: 237 type=190 (LJ14) 90 92
50: 238 type=195 (LJ14) 90 93
50: 239 type=186 (LJ14) 91 96
50: 240 type=186 (LJ14) 91 97
50: 241 type=209 (LJ14) 91 98
50: 242 type=188 (LJ14) 91 101
50: 243 type=189 (LJ14) 91 102
50: 244 type=190 (LJ14) 92 94
50: 245 type=190 (LJ14) 92 95
50: 246 type=190 (LJ14) 92 100
50: 247 type=190 (LJ14) 93 99
50: 248 type=190 (LJ14) 93 103
50: 249 type=192 (LJ14) 93 104
50: 250 type=193 (LJ14) 94 96
50: 251 type=193 (LJ14) 94 97
50: 252 type=210 (LJ14) 94 98
50: 253 type=194 (LJ14) 94 101
50: 254 type=186 (LJ14) 94 102
50: 255 type=195 (LJ14) 95 101
50: 256 type=187 (LJ14) 95 102
50: 257 type=190 (LJ14) 96 99
50: 258 type=196 (LJ14) 96 100
50: 259 type=190 (LJ14) 97 99
50: 260 type=196 (LJ14) 97 100
50: 261 type=211 (LJ14) 98 100
50: 262 type=196 (LJ14) 100 105
50: 263 type=197 (LJ14) 100 106
50: 264 type=198 (LJ14) 100 115
50: 265 type=190 (LJ14) 101 103
50: 266 type=195 (LJ14) 101 104
50: 267 type=186 (LJ14) 102 107
50: 268 type=186 (LJ14) 102 108
50: 269 type=187 (LJ14) 102 109
50: 270 type=188 (LJ14) 102 116
50: 271 type=189 (LJ14) 102 117
50: 272 type=190 (LJ14) 103 105
50: 273 type=190 (LJ14) 103 106
50: 274 type=190 (LJ14) 103 115
50: 275 type=191 (LJ14) 104 110
50: 276 type=191 (LJ14) 104 111
50: 277 type=197 (LJ14) 104 112
50: 278 type=190 (LJ14) 104 118
50: 279 type=192 (LJ14) 104 119
50: 280 type=193 (LJ14) 105 107
50: 281 type=193 (LJ14) 105 108
50: 282 type=191 (LJ14) 105 109
50: 283 type=194 (LJ14) 105 116
50: 284 type=186 (LJ14) 105 117
50: 285 type=195 (LJ14) 106 113
50: 286 type=195 (LJ14) 106 114
50: 287 type=195 (LJ14) 106 116
50: 288 type=187 (LJ14) 106 117
50: 289 type=193 (LJ14) 107 110
50: 290 type=193 (LJ14) 107 111
50: 291 type=196 (LJ14) 107 112
50: 292 type=196 (LJ14) 107 115
50: 293 type=193 (LJ14) 108 110
50: 294 type=193 (LJ14) 108 111
50: 295 type=196 (LJ14) 108 112
50: 296 type=196 (LJ14) 108 115
50: 297 type=197 (LJ14) 109 115
50: 298 type=194 (LJ14) 110 113
50: 299 type=194 (LJ14) 110 114
50: 300 type=194 (LJ14) 111 113
50: 301 type=194 (LJ14) 111 114
50: 302 type=196 (LJ14) 115 120
50: 303 type=197 (LJ14) 115 121
50: 304 type=198 (LJ14) 115 134
50: 305 type=190 (LJ14) 116 118
50: 306 type=195 (LJ14) 116 119
50: 307 type=186 (LJ14) 117 122
50: 308 type=186 (LJ14) 117 123
50: 309 type=187 (LJ14) 117 124
50: 310 type=188 (LJ14) 117 135
50: 311 type=189 (LJ14) 117 136
50: 312 type=190 (LJ14) 118 120
50: 313 type=190 (LJ14) 118 121
50: 314 type=190 (LJ14) 118 134
50: 315 type=191 (LJ14) 119 125
50: 316 type=192 (LJ14) 119 126
50: 317 type=192 (LJ14) 119 130
50: 318 type=190 (LJ14) 119 137
50: 319 type=192 (LJ14) 119 138
50: 320 type=193 (LJ14) 120 122
50: 321 type=193 (LJ14) 120 123
50: 322 type=191 (LJ14) 120 124
50: 323 type=194 (LJ14) 120 135
50: 324 type=186 (LJ14) 120 136
50: 325 type=191 (LJ14) 121 127
50: 326 type=191 (LJ14) 121 128
50: 327 type=191 (LJ14) 121 129
50: 328 type=191 (LJ14) 121 131
50: 329 type=191 (LJ14) 121 132
50: 330 type=191 (LJ14) 121 133
50: 331 type=195 (LJ14) 121 135
50: 332 type=187 (LJ14) 121 136
50: 333 type=193 (LJ14) 122 125
50: 334 type=191 (LJ14) 122 126
50: 335 type=191 (LJ14) 122 130
50: 336 type=196 (LJ14) 122 134
50: 337 type=193 (LJ14) 123 125
50: 338 type=191 (LJ14) 123 126
50: 339 type=191 (LJ14) 123 130
50: 340 type=196 (LJ14) 123 134
50: 341 type=197 (LJ14) 124 134
50: 342 type=193 (LJ14) 125 127
50: 343 type=193 (LJ14) 125 128
50: 344 type=193 (LJ14) 125 129
50: 345 type=193 (LJ14) 125 131
50: 346 type=193 (LJ14) 125 132
50: 347 type=193 (LJ14) 125 133
50: 348 type=191 (LJ14) 126 131
50: 349 type=191 (LJ14) 126 132
50: 350 type=191 (LJ14) 126 133
50: 351 type=191 (LJ14) 127 130
50: 352 type=191 (LJ14) 128 130
50: 353 type=191 (LJ14) 129 130
50: 354 type=196 (LJ14) 134 139
50: 355 type=197 (LJ14) 134 140
50: 356 type=198 (LJ14) 134 144
50: 357 type=190 (LJ14) 135 137
50: 358 type=195 (LJ14) 135 138
50: 359 type=186 (LJ14) 136 141
50: 360 type=186 (LJ14) 136 142
50: 361 type=186 (LJ14) 136 143
50: 362 type=188 (LJ14) 136 145
50: 363 type=189 (LJ14) 136 146
50: 364 type=190 (LJ14) 137 139
50: 365 type=190 (LJ14) 137 140
50: 366 type=190 (LJ14) 137 144
50: 367 type=190 (LJ14) 138 147
50: 368 type=192 (LJ14) 138 148
50: 369 type=193 (LJ14) 139 141
50: 370 type=193 (LJ14) 139 142
50: 371 type=193 (LJ14) 139 143
50: 372 type=194 (LJ14) 139 145
50: 373 type=186 (LJ14) 139 146
50: 374 type=195 (LJ14) 140 145
50: 375 type=187 (LJ14) 140 146
50: 376 type=196 (LJ14) 141 144
50: 377 type=196 (LJ14) 142 144
50: 378 type=196 (LJ14) 143 144
50: 379 type=196 (LJ14) 144 149
50: 380 type=197 (LJ14) 144 150
50: 381 type=198 (LJ14) 144 154
50: 382 type=190 (LJ14) 145 147
50: 383 type=195 (LJ14) 145 148
50: 384 type=186 (LJ14) 146 151
50: 385 type=186 (LJ14) 146 152
50: 386 type=186 (LJ14) 146 153
50: 387 type=188 (LJ14) 146 155
50: 388 type=190 (LJ14) 147 149
50: 389 type=190 (LJ14) 147 150
50: 390 type=190 (LJ14) 147 154
50: 391 type=193 (LJ14) 149 151
50: 392 type=193 (LJ14) 149 152
50: 393 type=193 (LJ14) 149 153
50: 394 type=194 (LJ14) 149 155
50: 395 type=195 (LJ14) 150 155
50: 396 type=196 (LJ14) 151 154
50: 397 type=196 (LJ14) 152 154
50: 398 type=196 (LJ14) 153 154
50: Coulomb-14:
50: nr: 0
50: LJC-14 q:
50: nr: 0
50: LJC Pairs NB:
50: nr: 0
50: LJ (SR):
50: nr: 0
50: Buck.ham (SR):
50: nr: 0
50: LJ (unused):
50: nr: 0
50: B.ham (unused):
50: nr: 0
50: Disper. corr.:
50: nr: 0
50: Coulomb (SR):
50: nr: 0
50: Coul (unused):
50: nr: 0
50: RF excl.:
50: nr: 0
50: Coul. recip.:
50: nr: 0
50: LJ recip.:
50: nr: 0
50: DPD:
50: nr: 0
50: Polarization:
50: nr: 0
50: Water Pol.:
50: nr: 0
50: Thole Pol.:
50: nr: 0
50: Anharm. Pol.:
50: nr: 0
50: Position Rest.:
50: nr: 0
50: Flat-bottom posres:
50: nr: 0
50: Dis. Rest.:
50: nr: 0
50: D.R.Viol. (nm):
50: nr: 0
50: Orient. Rest.:
50: nr: 0
50: Ori. R. RMSD:
50: nr: 0
50: Angle Rest.:
50: nr: 0
50: Angle Rest. Z:
50: nr: 0
50: Dih. Rest.:
50: nr: 0
50: Dih. Rest. Viol.:
50: nr: 0
50: Constraint:
50: nr: 0
50: Constr. No Conn.:
50: nr: 0
50: Settle:
50: nr: 0
50: Virtual site 1:
50: nr: 0
50: Virtual site 2:
50: nr: 0
50: Virtual site 2fd:
50: nr: 0
50: Virtual site 3:
50: nr: 0
50: Virtual site 3fd:
50: nr: 0
50: Virtual site 3fad:
50: nr: 0
50: Virtual site 3out:
50: nr: 0
50: Virtual site 4fd:
50: nr: 0
50: Virtual site 4fdn:
50: nr: 0
50: Virtual site N:
50: nr: 0
50: COM Pull En.:
50: nr: 0
50: Density fitting:
50: nr: 0
50: Quantum En.:
50: nr: 0
50: Potential:
50: nr: 0
50: Kinetic En.:
50: nr: 0
50: Total Energy:
50: nr: 0
50: Conserved En.:
50: nr: 0
50: Temperature:
50: nr: 0
50: Vir. Temp. (not used):
50: nr: 0
50: Pres. DC:
50: nr: 0
50: Pressure:
50: nr: 0
50: dH/dl constr.:
50: nr: 0
50: dVremain/dl:
50: nr: 0
50: dEkin/dl:
50: nr: 0
50: dVcoul/dl:
50: nr: 0
50: dVvdw/dl:
50: nr: 0
50: dVbonded/dl:
50: nr: 0
50: dVrestraint/dl:
50: nr: 0
50: dVtemperature/dl:
50: nr: 0
50: grp[T-Coupling ] nr=1, name=[ rest]
50: grp[Energy Mon. ] nr=1, name=[ rest]
50: grp[Acceleration] nr=1, name=[ rest]
50: grp[Freeze ] nr=1, name=[ rest]
50: grp[User1 ] nr=1, name=[ rest]
50: grp[User2 ] nr=1, name=[ rest]
50: grp[VCM ] nr=1, name=[ rest]
50: grp[Compressed X] nr=1, name=[ rest]
50: grp[Or. Res. Fit] nr=1, name=[ rest]
50: grp[QMMM ] nr=1, name=[ rest]
50: grpname (11):
50: grpname[0]={name="System"}
50: grpname[1]={name="Protein"}
50: grpname[2]={name="Protein-H"}
50: grpname[3]={name="C-alpha"}
50: grpname[4]={name="Backbone"}
50: grpname[5]={name="MainChain"}
50: grpname[6]={name="MainChain+Cb"}
50: grpname[7]={name="MainChain+H"}
50: grpname[8]={name="SideChain"}
50: grpname[9]={name="SideChain-H"}
50: grpname[10]={name="rest"}
50: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM
50: allocated 0 0 0 0 0 0 0 0 0 0
50: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0
50: box (3x3):
50: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00}
50: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00}
50: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00}
50: box_rel (3x3):
50: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: boxv (3x3):
50: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: pres_prev (3x3):
50: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: svir_prev (3x3):
50: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: fvir_prev (3x3):
50: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: nosehoover_xi: not available
50: x (156x3):
50: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00}
50: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00}
50: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00}
50: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00}
50: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00}
50: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00}
50: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00}
50: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00}
50: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01}
50: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01}
50: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01}
50: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00}
50: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01}
50: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01}
50: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01}
50: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01}
50: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01}
50: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01}
50: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01}
50: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01}
50: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01}
50: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01}
50: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00}
50: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00}
50: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00}
50: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00}
50: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00}
50: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01}
50: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00}
50: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00}
50: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00}
50: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00}
50: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01}
50: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01}
50: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00}
50: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00}
50: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00}
50: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00}
50: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01}
50: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01}
50: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01}
50: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01}
50: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01}
50: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01}
50: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01}
50: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01}
50: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01}
50: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01}
50: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01}
50: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01}
50: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01}
50: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01}
50: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01}
50: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01}
50: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01}
50: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01}
50: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01}
50: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01}
50: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01}
50: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01}
50: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01}
50: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01}
50: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01}
50: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01}
50: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01}
50: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01}
50: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01}
50: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01}
50: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01}
50: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01}
50: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01}
50: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01}
50: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01}
50: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01}
50: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02}
50: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02}
50: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02}
50: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02}
50: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02}
50: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01}
50: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02}
50: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01}
50: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02}
50: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01}
50: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01}
50: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01}
50: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02}
50: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01}
50: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02}
50: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01}
50: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02}
50: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01}
50: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01}
50: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02}
50: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02}
50: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02}
50: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01}
50: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02}
50: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02}
50: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02}
50: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02}
50: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02}
50: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01}
50: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01}
50: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01}
50: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01}
50: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01}
50: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01}
50: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01}
50: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01}
50: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01}
50: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01}
50: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01}
50: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01}
50: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01}
50: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01}
50: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01}
50: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01}
50: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01}
50: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01}
50: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01}
50: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01}
50: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01}
50: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01}
50: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01}
50: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02}
50: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01}
50: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01}
50: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01}
50: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01}
50: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01}
50: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01}
50: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01}
50: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01}
50: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02}
50: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02}
50: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02}
50: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02}
50: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01}
50: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01}
50: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01}
50: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01}
50: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01}
50: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01}
50: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01}
50: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01}
50: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01}
50: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01}
50: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01}
50: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01}
50: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01}
50: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01}
50: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01}
50: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02}
50: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01}
50: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01}
50: v (156x3):
50: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: Group statistics
50: T-Coupling : 156 (total 156 atoms)
50: Energy Mon. : 156 (total 156 atoms)
50: Acceleration: 156 (total 156 atoms)
50: Freeze : 156 (total 156 atoms)
50: User1 : 156 (total 156 atoms)
50: User2 : 156 (total 156 atoms)
50: VCM : 156 (total 156 atoms)
50: Compressed X: 156 (total 156 atoms)
50: Or. Res. Fit: 156 (total 156 atoms)
50: QMMM : 156 (total 156 atoms)
50: [ OK ] DumpTest.WorksWithTpr (49 ms)
50: [ RUN ] DumpTest.WorksWithTprAndMdpWriting
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
50: [ OK ] DumpTest.WorksWithTprAndMdpWriting (8 ms)
50: [----------] 2 tests from DumpTest (57 ms total)
50:
50: [----------] 3 tests from HelpwritingTest
50: [ RUN ] HelpwritingTest.ConvertTprWritesHelp
50: [ OK ] HelpwritingTest.ConvertTprWritesHelp (40 ms)
50: [ RUN ] HelpwritingTest.DumpWritesHelp
50: [ OK ] HelpwritingTest.DumpWritesHelp (12 ms)
50: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp
50: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (1 ms)
50: [----------] 3 tests from HelpwritingTest (53 ms total)
50:
50: [----------] 4 tests from ReportMethodsTest
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
50: For a correct single-point energy evaluation with nsteps = 0, use
50: continuation = yes to avoid constraining the input coordinates.
50:
50: Generating 1-4 interactions: fudge = 0.5
50:
50: NOTE 2 [file lysozyme.top, line 1465]:
50: System has non-zero total charge: 2.000000
50: Total charge should normally be an integer. See
50: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
50: for discussion on how close it should be to an integer.
50:
50:
50:
50: Number of degrees of freedom in T-Coupling group rest is 465.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
50: NVE simulation with an initial temperature of zero: will use a Verlet
50: buffer of 10%. Check your energy drift!
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Setting the LD random seed to -4982289
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50:
50: Generated 330891 of the 330891 1-4 parameter combinations
50:
50: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
50: Analysing residue names:
50: There are: 10 Protein residues
50: Analysing Protein...
50:
50: This run will generate roughly 0 Mb of data
50: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
50: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms)
50: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
50: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms)
50: [ RUN ] ReportMethodsTest.WritesCorrectInformation
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
50: [ OK ] ReportMethodsTest.WritesCorrectInformation (5 ms)
50: [ RUN ] ReportMethodsTest.ToolEndToEndTest
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
50: section: Methods
50: subsection: Simulation system
50: A system of 1 molecules (156 atoms) was simulated.
50:
50: subsection: Simulation settings
50: A total of 0 ns were simulated with a time step of 1 fs.
50: Neighbor searching was performed every 10 steps.
50: The Cut-off algorithm was used for electrostatic interactions.
50: with a cut-off of 1 nm.
50: A single cut-off of 1.1 nm was used for Van der Waals interactions.
50: [ OK ] ReportMethodsTest.ToolEndToEndTest (5 ms)
50: [----------] 4 tests from ReportMethodsTest (10 ms total)
50:
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: trr version: GMX_trn_file (single precision)
50:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (15 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (14 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (13 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from gro file '', 6 atoms.
50:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (14 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
50: -> frame 0 time 0.000
't= 0.00000', 6 atoms
50:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (14 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (13 ms)
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (84 ms total)
50:
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (4 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (5 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (4 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from gro file '', 6 atoms.
50:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (4 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
50: -> frame 0 time 0.000
't= 0.00000', 6 atoms
50:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (4 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (4 ms)
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (25 ms total)
50:
50: [----------] Global test environment tear-down
50: [==========] 21 tests from 5 test cases ran. (8975 ms total)
50: [ PASSED ] 21 tests.
50/65 Test #50: ToolUnitTests ......................... Passed 9.07 sec
test 51
Start 51: FileIOTests
51: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/FileIOTests.xml"
51: Test timeout computed to be: 30
51: [==========] Running 42 tests from 10 test cases.
51: [----------] Global test environment set-up.
51: [----------] 4 tests from Checkpoint
51: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent
51: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms)
51: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent
51: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms)
51: [ RUN ] Checkpoint.KvtRoundTripInt64
51: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms)
51: [ RUN ] Checkpoint.KvtRoundTripReal
51: [ OK ] Checkpoint.KvtRoundTripReal (0 ms)
51: [----------] 4 tests from Checkpoint (2 ms total)
51:
51: [----------] 2 tests from FileMD5Test
51: [ RUN ] FileMD5Test.CanComputeMD5
51: [ OK ] FileMD5Test.CanComputeMD5 (4 ms)
51: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
51: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms)
51: [----------] 2 tests from FileMD5Test (7 ms total)
51:
51: [----------] 3 tests from MrcSerializer
51: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet
51: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms)
51: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize
51: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms)
51: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip
51: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (4 ms)
51: [----------] 3 tests from MrcSerializer (6 ms total)
51:
51: [----------] 4 tests from MrcDensityMap
51: [ RUN ] MrcDensityMap.RoundTripIsIdempotent
51: [ OK ] MrcDensityMap.RoundTripIsIdempotent (4 ms)
51: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent
51: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms)
51: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile
51: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms)
51: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile
51: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (7 ms)
51: [----------] 4 tests from MrcDensityMap (16 ms total)
51:
51: [----------] 8 tests from MrcDensityMapHeaderTest
51: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader
51: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (1 ms)
51: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect
51: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid
51: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (1 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.IsSane
51: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms)
51: [----------] 8 tests from MrcDensityMapHeaderTest (5 ms total)
51:
51: [----------] 10 tests from ReadTest
51: [ RUN ] ReadTest.get_eint_ReadsInteger
51: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
51: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side '0.8' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms)
51: [ RUN ] ReadTest.get_eint_WarnsAboutString
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side 'hello' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
51: [ RUN ] ReadTest.get_eint64_ReadsInteger
51: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
51: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side '0.8' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms)
51: [ RUN ] ReadTest.get_eint64_WarnsAboutString
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side 'hello' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
51: [ RUN ] ReadTest.get_ereal_ReadsInteger
51: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
51: [ RUN ] ReadTest.get_ereal_ReadsFloat
51: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
51: [ RUN ] ReadTest.get_ereal_WarnsAboutString
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side 'hello' for parameter 'test' in parameter file is not a
51: real value
51:
51:
51: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
51: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString
51: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms)
51: [----------] 10 tests from ReadTest (5 ms total)
51:
51: [----------] 1 test from FileIOXdrSerializerTest
51: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect
51: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (1 ms)
51: [----------] 1 test from FileIOXdrSerializerTest (2 ms total)
51:
51: [----------] 2 tests from TngTest
51: [ RUN ] TngTest.CanOpenTngFile
51: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
51: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
51: [ OK ] TngTest.CanOpenTngFile (0 ms)
51: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
51: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
51: [----------] 2 tests from TngTest (0 ms total)
51:
51: [----------] 4 tests from XvgioTest
51: [ RUN ] XvgioTest.readXvgIntWorks
51: [ OK ] XvgioTest.readXvgIntWorks (3 ms)
51: [ RUN ] XvgioTest.readXvgRealWorks
51: [ OK ] XvgioTest.readXvgRealWorks (4 ms)
51: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks
51: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (1 ms)
51: [ RUN ] XvgioTest.readXvgDeprecatedWorks
51: [ OK ] XvgioTest.readXvgDeprecatedWorks (1 ms)
51: [----------] 4 tests from XvgioTest (9 ms total)
51:
51: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (3 ms)
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (3 ms)
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (10 ms)
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (2 ms)
51: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (19 ms total)
51:
51: [----------] Global test environment tear-down
51: [==========] 42 tests from 10 test cases ran. (74 ms total)
51: [ PASSED ] 42 tests.
51/65 Test #51: FileIOTests ........................... Passed 0.17 sec
test 52
Start 52: SelectionUnitTests
52: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml"
52: Test timeout computed to be: 30
52: [==========] Running 192 tests from 11 test cases.
52: [----------] Global test environment set-up.
52: [----------] 1 test from IndexGroupTest
52: [ RUN ] IndexGroupTest.RemovesDuplicates
52: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
52: [----------] 1 test from IndexGroupTest (0 ms total)
52:
52: [----------] 15 tests from IndexBlockTest
52: [ RUN ] IndexBlockTest.CreatesUnknownBlock
52: [ OK ] IndexBlockTest.CreatesUnknownBlock (10 ms)
52: [ RUN ] IndexBlockTest.CreatesAtomBlock
52: [ OK ] IndexBlockTest.CreatesAtomBlock (1 ms)
52: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology
52: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (2 ms)
52: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology
52: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (22 ms)
52: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology
52: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms)
52: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology
52: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (1 ms)
52: [ RUN ] IndexBlockTest.CreatesSingleBlock
52: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
52: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
52: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (1 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
52: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (1 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms)
52: [----------] 15 tests from IndexBlockTest (41 ms total)
52:
52: [----------] 11 tests from IndexMapTest
52: [ RUN ] IndexMapTest.InitializesAtomBlock
52: [ OK ] IndexMapTest.InitializesAtomBlock (2 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
52: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (1 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
52: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (1 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
52: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (1 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
52: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (1 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
52: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (1 ms)
52: [ RUN ] IndexMapTest.InitializesMoleculeBlock
52: [ OK ] IndexMapTest.InitializesMoleculeBlock (1 ms)
52: [ RUN ] IndexMapTest.MapsSingleBlock
52: [ OK ] IndexMapTest.MapsSingleBlock (2 ms)
52: [ RUN ] IndexMapTest.MapsResidueBlocks
52: [ OK ] IndexMapTest.MapsResidueBlocks (1 ms)
52: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
52: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (2 ms)
52: [ RUN ] IndexMapTest.HandlesMultipleRequests
52: [ OK ] IndexMapTest.HandlesMultipleRequests (11 ms)
52: [----------] 11 tests from IndexMapTest (26 ms total)
52:
52: [----------] 3 tests from IndexGroupsAndNamesTest
52: [ RUN ] IndexGroupsAndNamesTest.containsNames
52: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms)
52: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing
52: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (1 ms)
52: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect
52: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms)
52: [----------] 3 tests from IndexGroupsAndNamesTest (1 ms total)
52:
52: [----------] 15 tests from NeighborhoodSearchTest
52: [ RUN ] NeighborhoodSearchTest.SimpleSearch
52: [ OK ] NeighborhoodSearchTest.SimpleSearch (74 ms)
52: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
52: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (81 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchBox
52: [ OK ] NeighborhoodSearchTest.GridSearchBox (14 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
52: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (48 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
52: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (24 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
52: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (14 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
52: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (14 ms)
52: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
52: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (1 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
52: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (219 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
52: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (1 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
52: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
52: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
52: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms)
52: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
52: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (18 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
52: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (5 ms)
52: [----------] 15 tests from NeighborhoodSearchTest (514 ms total)
52:
52: [----------] 12 tests from PositionCalculationTest
52: [ RUN ] PositionCalculationTest.ComputesAtomPositions
52: [ OK ] PositionCalculationTest.ComputesAtomPositions (3 ms)
52: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
52: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (2 ms)
52: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
52: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (37 ms)
52: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
52: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (1 ms)
52: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
52: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (9 ms)
52: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
52: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (1 ms)
52: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
52: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (1 ms)
52: [ RUN ] PositionCalculationTest.ComputesPositionMask
52: [ OK ] PositionCalculationTest.ComputesPositionMask (19 ms)
52: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
52: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (1 ms)
52: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
52: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (1 ms)
52: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
52: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (2 ms)
52: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
52: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (5 ms)
52: [----------] 12 tests from PositionCalculationTest (86 ms total)
52:
52: [----------] 29 tests from SelectionCollectionTest
52: [ RUN ] SelectionCollectionTest.HandlesNoSelections
52: [ OK ] SelectionCollectionTest.HandlesNoSelections (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
52: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (3 ms)
52: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
52: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
52: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (2 ms)
52: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
52: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
52: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
52: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
52: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
52: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
52: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (3 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
52: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (3 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
52: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
52: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
52: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
52: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
52: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (2 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
52: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (2 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
52: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (2 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
52: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (2 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
52: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
52: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (3 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (2 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (3 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (2 ms)
52: [----------] 29 tests from SelectionCollectionTest (60 ms total)
52:
52: [----------] 14 tests from SelectionCollectionInteractiveTest
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (4 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
52: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
52: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (4 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
52: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (4 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
52: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
52: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
52: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
52: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
52: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
52: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (3 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
52: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (2 ms)
52: [----------] 14 tests from SelectionCollectionInteractiveTest (44 ms total)
52:
52: [----------] 66 tests from SelectionCollectionDataTest
52: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
52: [ OK ] SelectionCollectionDataTest.HandlesAllNone (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
52: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesResnr
52: [ OK ] SelectionCollectionDataTest.HandlesResnr (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
52: [ OK ] SelectionCollectionDataTest.HandlesResIndex (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
52: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
52: [ OK ] SelectionCollectionDataTest.HandlesAtomname (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
52: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
52: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesChain
52: [ OK ] SelectionCollectionDataTest.HandlesChain (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMass
52: [ OK ] SelectionCollectionDataTest.HandlesMass (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesCharge
52: [ OK ] SelectionCollectionDataTest.HandlesCharge (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
52: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
52: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
52: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBeta
52: [ OK ] SelectionCollectionDataTest.HandlesBeta (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesResname
52: [ OK ] SelectionCollectionDataTest.HandlesResname (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
52: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
52: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
52: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
52: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (9 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (27 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
52: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (11 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
52: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (11 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
52: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (12 ms)
52: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
52: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (9 ms)
52: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
52: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
52: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (7 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
52: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
52: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
52: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
52: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (8 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
52: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (8 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
52: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
52: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
52: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
52: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
52: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
52: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (9 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
52: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
52: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
52: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
52: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (9 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
52: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
52: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
52: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
52: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
52: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (20 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
52: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
52: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (8 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
52: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (14 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
52: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (7 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
52: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (12 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
52: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (7 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
52: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
52: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
52: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (8 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
52: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
52: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
52: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
52: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
52: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (7 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
52: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (14 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
52: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (5 ms)
52: [----------] 66 tests from SelectionCollectionDataTest (418 ms total)
52:
52: [----------] 17 tests from SelectionOptionTest
52: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
52: [ OK ] SelectionOptionTest.ParsesSimpleSelection (2 ms)
52: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
52: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
52: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (4 ms)
52: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
52: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (2 ms)
52: [ RUN ] SelectionOptionTest.ChecksEmptySelections
52: [ OK ] SelectionOptionTest.ChecksEmptySelections (2 ms)
52: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
52: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooManySelections
52: [ OK ] SelectionOptionTest.HandlesTooManySelections (2 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
52: [ OK ] SelectionOptionTest.HandlesTooFewSelections (2 ms)
52: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
52: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesAdjuster
52: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (2 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (2 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
52: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
52: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (2 ms)
52: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
52: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (2 ms)
52: [----------] 17 tests from SelectionOptionTest (37 ms total)
52:
52: [----------] 9 tests from SelectionFileOptionTest
52: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
52: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (2 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
52: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (2 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
52: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (2 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
52: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (2 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
52: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (2 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
52: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (2 ms)
52: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
52: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
52: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (2 ms)
52: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
52: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (2 ms)
52: [----------] 9 tests from SelectionFileOptionTest (17 ms total)
52:
52: [----------] Global test environment tear-down
52: [==========] 192 tests from 11 test cases ran. (1245 ms total)
52: [ PASSED ] 192 tests.
52/65 Test #52: SelectionUnitTests .................... Passed 1.37 sec
test 53
Start 53: MdrunOutputTests
53: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml"
53: Test timeout computed to be: 600
53: [==========] Running 12 tests from 5 test cases.
53: [----------] Global test environment set-up.
53: [----------] 1 test from MdrunTest
53: [ RUN ] MdrunTest.WritesHelp
53: [ OK ] MdrunTest.WritesHelp (84 ms)
53: [----------] 1 test from MdrunTest (84 ms total)
53:
53: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
53: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
53: Generating 1-4 interactions: fudge = 0.5
53: Number of degrees of freedom in T-Coupling group rest is 9.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
53: NVE simulation: will use the initial temperature of 2573.591 K for
53: determining the Verlet buffer size
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc2'
53: 1 steps, 0.0 ps.
53: Setting the LD random seed to -20974915
53:
53: Generated 3 of the 3 non-bonded parameter combinations
53:
53: Generated 3 of the 3 1-4 parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.351 0.176 199.7
53: (ns/day) (hour/ns)
53: Performance: 0.982 24.446
53:
Reading frame 0 time 0.000
53: # Atoms 6
53:
Reading frame 1 time 0.001
Last frame 1 time 0.001
53:
53:
53: Item #frames Timestep (ps)
53: Step 2 0.001
53: Time 2 0.001
53: Lambda 0
53: Coords 2 0.001
53: Velocities 0
53: Forces 0
53: Box 2 0.001
53: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
53: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (228 ms)
53: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
53: Generating 1-4 interactions: fudge = 0.5
53: Number of degrees of freedom in T-Coupling group rest is 9.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
53: NVE simulation: will use the initial temperature of 2573.591 K for
53: determining the Verlet buffer size
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc2'
53: 1 steps, 0.0 ps.
53: Setting the LD random seed to 1580711902
53:
53: Generated 3 of the 3 non-bonded parameter combinations
53:
53: Generated 3 of the 3 1-4 parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.346 0.174 199.7
53: (ns/day) (hour/ns)
53: Performance: 0.996 24.102
53:
Reading frame 0 time 0.000
53: # Atoms 6
53:
Reading frame 1 time 0.001
Last frame 1 time 0.001
53:
53:
53: Item #frames Timestep (ps)
53: Step 2 0.001
53: Time 2 0.001
53: Lambda 0
53: Coords 2 0.001
53: Velocities 0
53: Forces 0
53: Box 2 0.001
53: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
53: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (208 ms)
53: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
53: Generating 1-4 interactions: fudge = 0.5
53: Number of degrees of freedom in T-Coupling group rest is 9.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
53: NVE simulation: will use the initial temperature of 2573.591 K for
53: determining the Verlet buffer size
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc2'
53: 1 steps, 0.0 ps.
53: Setting the LD random seed to -35835530
53:
53: Generated 3 of the 3 non-bonded parameter combinations
53:
53: Generated 3 of the 3 1-4 parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.329 0.165 199.6
53: (ns/day) (hour/ns)
53: Performance: 1.048 22.903
53:
Reading frame 0 time 0.000
53: # Atoms 3
53:
Reading frame 1 time 0.001
Last frame 1 time 0.001
53:
53:
53: Item #frames Timestep (ps)
53: Step 2 0.001
53: Time 2 0.001
53: Lambda 0
53: Coords 2 0.001
53: Velocities 0
53: Forces 0
53: Box 2 0.001
53: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
53: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (199 ms)
53: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (636 ms total)
53:
53: [----------] 2 tests from Argon12/OutputFiles
53: [ RUN ] Argon12/OutputFiles.FilesArePresent/0
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
53: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
53: that with the Verlet scheme, nstlist has no effect on the accuracy of
53: your simulation.
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
53: Setting nstcalcenergy (100) equal to nstenergy (4)
53:
53: Number of degrees of freedom in T-Coupling group System is 33.00
53:
53: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
53: NVE simulation: will use the initial temperature of 68.810 K for
53: determining the Verlet buffer size
53:
53:
53: There were 3 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'Argon'
53: 16 steps, 0.0 ps.
53: Generated 1 of the 1 non-bonded parameter combinations
53:
53: Excluding 1 bonded neighbours molecule type 'Argon'
53:
53: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
53:
53: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 1.061 0.531 199.9
53: (ns/day) (hour/ns)
53: Performance: 2.768 8.670
53: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (567 ms)
53: [ RUN ] Argon12/OutputFiles.FilesArePresent/1
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
53: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
53: that with the Verlet scheme, nstlist has no effect on the accuracy of
53: your simulation.
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
53: Setting nstcalcenergy (100) equal to nstenergy (4)
53:
53: Number of degrees of freedom in T-Coupling group System is 33.00
53:
53: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
53: NVE simulation: will use the initial temperature of 68.810 K for
53: determining the Verlet buffer size
53:
53:
53: There were 3 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'Argon'
53: 16 steps, 0.0 ps.
53: Generated 1 of the 1 non-bonded parameter combinations
53:
53: Excluding 1 bonded neighbours molecule type 'Argon'
53:
53: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
53:
53: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.405 0.203 199.8
53: (ns/day) (hour/ns)
53: Performance: 7.244 3.313
53: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (243 ms)
53: [----------] 2 tests from Argon12/OutputFiles (812 ms total)
53:
53: [----------] 3 tests from MdrunCanWrite/Trajectories
53: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 6 steps, 0.0 ps.
53: Setting the LD random seed to 1518266303
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.301 0.151 199.5
53: (ns/day) (hour/ns)
53: Performance: 4.011 5.984
53: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (199 ms)
53: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 6 steps, 0.0 ps.
53: Setting the LD random seed to -274477313
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.306 0.153 199.5
53: (ns/day) (hour/ns)
53: Performance: 3.943 6.087
53: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (200 ms)
53: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 6 steps, 0.0 ps.
53: Setting the LD random seed to -538610693
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.306 0.153 199.5
53: (ns/day) (hour/ns)
53: Performance: 3.944 6.085
53: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (200 ms)
53: [----------] 3 tests from MdrunCanWrite/Trajectories (599 ms total)
53:
53: [----------] 3 tests from MdrunCanWrite/NptTrajectories
53: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 2 steps, 0.0 ps.
53: Setting the LD random seed to -281023623
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.303 0.152 199.5
53: (ns/day) (hour/ns)
53: Performance: 1.707 14.063
53: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (203 ms)
53: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 2 steps, 0.0 ps.
53: Setting the LD random seed to 2042626001
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.268 0.134 199.4
53: (ns/day) (hour/ns)
53: Performance: 1.929 12.443
53: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (180 ms)
53: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 2 steps, 0.0 ps.
53: Setting the LD random seed to -151785473
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.264 0.133 199.4
53: (ns/day) (hour/ns)
53: Performance: 1.956 12.270
53: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (176 ms)
53: [----------] 3 tests from MdrunCanWrite/NptTrajectories (561 ms total)
53:
53: [----------] Global test environment tear-down
53: [==========] 12 tests from 5 test cases ran. (2835 ms total)
53: [ PASSED ] 12 tests.
53/65 Test #53: MdrunOutputTests ...................... Passed 2.91 sec
test 54
Start 54: MdrunModulesTests
54: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml"
54: Test timeout computed to be: 600
54: [==========] Running 15 tests from 3 test cases.
54: [----------] Global test environment set-up.
54: [----------] 9 tests from DensityFittingTest
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -3.85654101644806e+03
54: Maximum force = 2.88468568366558e+03 on atom 3
54: Norm of force = 1.07544474716821e+03
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to 2143223807
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (69 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -9.82084736967821e+03
54: Maximum force = 4.73310933913648e+03 on atom 2
54: Norm of force = 1.78012183879532e+03
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to 1245626351
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (45 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff
54:
54: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1050:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out.
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (33 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -9.76043429797377e+03
54: Maximum force = 4.63447892024619e+03 on atom 2
54: Norm of force = 1.75756003355952e+03
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to -1250600962
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (38 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff
54:
54: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1050:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out.
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (32 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -3.85654101644806e+03
54: Maximum force = 2.88468568366558e+03 on atom 3
54: Norm of force = 1.07544474716821e+03
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to -268641069
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (45 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -2.71386626596691e+04
54: Maximum force = 4.34097106676756e+03 on atom 2
54: Norm of force = 1.25497916295893e+03
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to 1608744441
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (44 ms)
54: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch
54:
54: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1050:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out.
54: Setting the LD random seed to 1597317116
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (36 ms)
54: [ RUN ] DensityFittingTest.CheckpointWorks
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
54: Setting nstcalcenergy (100) equal to nstenergy (2)
54:
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
54: NVE simulation: will use the initial temperature of 68.810 K for
54: determining the Verlet buffer size
54:
54:
54: There were 2 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting mdrun 'Argon'
54: 2 steps, 0.0 ps.
54: Setting the LD random seed to -1090595689
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K
54:
54: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
54:
54: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
54:
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54:
54: This run will generate roughly 0 Mb of data
54:
54: Writing final coordinates.
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.293 0.147 199.6
54: (ns/day) (hour/ns)
54: Performance: 1.767 13.585
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
54: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps
54: Can not increase nstlist because an NVE ensemble is used
54:
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting mdrun 'Argon'
54: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps).
54:
54: Writing final coordinates.
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.288 0.144 199.6
54: (ns/day) (hour/ns)
54: Performance: 2.998 8.004
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (338 ms)
54: [----------] 9 tests from DensityFittingTest (683 ms total)
54:
54: [----------] 4 tests from MimicTest
54: [ RUN ] MimicTest.OneQuantumMol
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 21.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
54: NVE simulation with an initial temperature of zero: will use a Verlet
54: buffer of 10%. Check your energy drift!
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
54:
54: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.003 0.001 184.6
54: (ns/day) (hour/ns)
54: Performance: 62.202 0.386
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 1275067335
54:
54: Generated 10 of the 10 non-bonded parameter combinations
54:
54: Generated 10 of the 10 1-4 parameter combinations
54:
54: Excluding 2 bonded neighbours molecule type 'SOL'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.OneQuantumMol (36 ms)
54: [ RUN ] MimicTest.AllQuantumMol
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 21.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
54: NVE simulation with an initial temperature of zero: will use a Verlet
54: buffer of 10%. Check your energy drift!
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
54:
54: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.003 0.001 184.1
54: (ns/day) (hour/ns)
54: Performance: 62.936 0.381
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -543220245
54:
54: Generated 10 of the 10 non-bonded parameter combinations
54:
54: Generated 10 of the 10 1-4 parameter combinations
54:
54: Excluding 2 bonded neighbours molecule type 'SOL'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.AllQuantumMol (35 ms)
54: [ RUN ] MimicTest.TwoQuantumMol
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 21.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
54: NVE simulation with an initial temperature of zero: will use a Verlet
54: buffer of 10%. Check your energy drift!
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
54:
54: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.003 0.001 184.3
54: (ns/day) (hour/ns)
54: Performance: 63.633 0.377
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -1900292353
54:
54: Generated 10 of the 10 non-bonded parameter combinations
54:
54: Generated 10 of the 10 1-4 parameter combinations
54:
54: Excluding 2 bonded neighbours molecule type 'SOL'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.TwoQuantumMol (34 ms)
54: [ RUN ] MimicTest.BondCuts
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 66.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
54: NVE simulation: will use the initial temperature of 300.368 K for
54: determining the Verlet buffer size
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
54:
54: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.005 0.003 190.9
54: (ns/day) (hour/ns)
54: Performance: 33.859 0.709
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 2063416317
54:
54: Generated 2211 of the 2211 non-bonded parameter combinations
54:
54: Generated 2211 of the 2211 1-4 parameter combinations
54:
54: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
54:
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
54:
54: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
54:
54: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
54:
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.BondCuts (214 ms)
54: [----------] 4 tests from MimicTest (319 ms total)
54:
54: [----------] 2 tests from WithIntegrator/ImdTest
54: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0
54: Generating 1-4 interactions: fudge = 1
54:
54: NOTE 1 [file glycine_vacuo.top, line 12]:
54: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an
54: estimated oscillational period of 1.0e-02 ps, which is less than 10 times
54: the time step of 2.0e-03 ps.
54: Maybe you forgot to change the constraints mdp option.
54:
54: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
54: Number of degrees of freedom in T-Coupling group System is 27.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
54: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34
54:
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: IMD: Enabled. This simulation will accept incoming IMD connections.
54: IMD: Pulling from IMD remote is enabled (-imdpull).
54: IMD: Setting port for connection requests to 0.
54: IMD: Setting up incoming socket.
54: IMD: Listening for IMD connection on port 34335.
54: IMD: -imdwait not set, starting simulation.
54: starting mdrun 'Glycine'
54: 2 steps, 0.0 ps.
54: Setting the LD random seed to -1357004818
54:
54: Generated 20503 of the 20503 non-bonded parameter combinations
54:
54: Generated 17396 of the 20503 1-4 parameter combinations
54:
54: Excluding 3 bonded neighbours molecule type 'Glycine'
54:
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
54:
54: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
54:
54: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm
54:
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54:
54: This run will generate roughly 0 Mb of data
54:
54: Writing final coordinates.
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.473 0.237 199.6
54: (ns/day) (hour/ns)
54: Performance: 2.186 10.979
54: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (1373 ms)
54: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
54: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not
54: apply to steep.
54:
54: Generating 1-4 interactions: fudge = 1
54: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
54: Number of degrees of freedom in T-Coupling group System is 27.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: IMD: Enabled. This simulation will accept incoming IMD connections.
54: IMD: Pulling from IMD remote is enabled (-imdpull).
54: IMD: Setting port for connection requests to 0.
54: IMD: Setting up incoming socket.
54: IMD: Listening for IMD connection on port 58015.
54: IMD: -imdwait not set, starting simulation.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = 1.19770464690297e+03
54: Maximum force = 1.77948604657896e+04 on atom 9
54: Norm of force = 7.87328617833980e+03
54: Setting the LD random seed to -25169953
54:
54: Generated 20503 of the 20503 non-bonded parameter combinations
54:
54: Generated 17396 of the 20503 1-4 parameter combinations
54:
54: Excluding 3 bonded neighbours molecule type 'Glycine'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (1042 ms)
54: [----------] 2 tests from WithIntegrator/ImdTest (2415 ms total)
54:
54: [----------] Global test environment tear-down
54: [==========] 15 tests from 3 test cases ran. (3528 ms total)
54: [ PASSED ] 15 tests.
54/65 Test #54: MdrunModulesTests ..................... Passed 3.61 sec
test 55
Start 55: MdrunIOTests
55: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunIOTests.xml"
55: Test timeout computed to be: 600
55: [==========] Running 61 tests from 10 test cases.
55: [----------] Global test environment set-up.
55: [----------] 3 tests from GromppTest
55: [ RUN ] GromppTest.EmptyMdpFileWorks
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
55: For a correct single-point energy evaluation with nsteps = 0, use
55: continuation = yes to avoid constraining the input coordinates.
55:
55: Number of degrees of freedom in T-Coupling group rest is 12.00
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
55: NVE simulation: will use the initial temperature of 1046.791 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Setting the LD random seed to -774504609
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: [ OK ] GromppTest.EmptyMdpFileWorks (27 ms)
55: [ RUN ] GromppTest.SimulatedAnnealingWorks
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
55: For a correct single-point energy evaluation with nsteps = 0, use
55: continuation = yes to avoid constraining the input coordinates.
55:
55: Simulated annealing for group rest: Periodic, 4 timepoints
55: Time (ps) Temperature (K)
55: 0.0 298.0
55: 2.0 320.0
55: 4.0 320.0
55: 6.0 298.0
55: Number of degrees of freedom in T-Coupling group rest is 12.00
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
55: NVE simulation: will use the initial temperature of 1046.791 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Setting the LD random seed to -1227129009
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: [ OK ] GromppTest.SimulatedAnnealingWorks (23 ms)
55: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
55: For a correct single-point energy evaluation with nsteps = 0, use
55: continuation = yes to avoid constraining the input coordinates.
55:
55: Simulated annealing for group Methanol: Single, 3 timepoints
55: Time (ps) Temperature (K)
55: 0.0 298.0
55: 3.0 280.0
55: 6.0- 270.0
55: Simulated annealing for group SOL: Periodic, 4 timepoints
55: Time (ps) Temperature (K)
55: 0.0 298.0
55: 2.0 320.0
55: 4.0 320.0
55: 6.0 298.0
55: Number of degrees of freedom in T-Coupling group Methanol is 7.20
55: Number of degrees of freedom in T-Coupling group SOL is 4.80
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
55: NVE simulation: will use the initial temperature of 1046.791 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Setting the LD random seed to -104925394
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (22 ms)
55: [----------] 3 tests from GromppTest (73 ms total)
55:
55: [----------] 6 tests from MdrunTerminationTest
55: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -1909463241
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.339 0.170 199.7
55: (ns/day) (hour/ns)
55: Performance: 1.526 15.724
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.319 0.160 199.7
55: (ns/day) (hour/ns)
55: Performance: 1.624 14.775
55: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (385 ms)
55: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 10 to 1, rlist from 1.024 to 1
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 100 steps, 0.1 ps.
55:
55: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps
55: Setting the LD random seed to -46399713
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.327 0.164 199.6
55: (ns/day) (hour/ns)
55: Performance: 1.581 15.181
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Setting nsteps to 102
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 102 steps, 0.1 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 100
55: Runtime for the run 0.1 ps
55: Run end step 100
55: Run end time 0.1 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 102
55: Runtime for the run 0.102 ps
55: Run end step 102
55: Run end time 0.102 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.320 0.160 199.6
55: (ns/day) (hour/ns)
55: Performance: 54.440 0.441
55: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (378 ms)
55: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -1158159465
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.328 0.164 199.6
55: (ns/day) (hour/ns)
55: Performance: 1.580 15.195
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.416 0.208 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.244 19.294
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Setting nsteps to 6
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 6
55: Runtime for the run 0.006 ps
55: Run end step 6
55: Run end time 0.006 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.371 0.186 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.396 17.198
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Setting nsteps to 8
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 6
55: Runtime for the run 0.006 ps
55: Run end step 6
55: Run end time 0.006 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 8
55: Runtime for the run 0.008 ps
55: Run end step 8
55: Run end time 0.008 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.282 0.141 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.839 13.052
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.001 0.001 163.6
55: (ns/day) (hour/ns)
55: Performance: 106.148 0.226
55: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (831 ms)
55: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -31460057
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.309 0.155 199.6
55: (ns/day) (hour/ns)
55: Performance: 1.675 14.330
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps.
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.260 0.130 199.4
55: (ns/day) (hour/ns)
55: Performance: 3.312 7.247
55: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (336 ms)
55: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -2916353
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.238 0.119 199.5
55: (ns/day) (hour/ns)
55: Performance: 2.173 11.042
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Setting nsteps to 4
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (158 ms)
55: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to 2117590481
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.280 0.140 199.6
55: (ns/day) (hour/ns)
55: Performance: 1.847 12.994
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.288 0.144 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.797 13.358
55: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (338 ms)
55: [----------] 6 tests from MdrunTerminationTest (2427 ms total)
55:
55: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks
55: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.419 0.210 199.7
55: (ns/day) (hour/ns)
55: Performance: 7.004 3.426
55: trr version: GMX_trn_file (double precision)
55:
55:
55: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (266 ms)
55: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.436 0.218 199.9
55: (ns/day) (hour/ns)
55: Performance: 6.729 3.567
55:
55:
55: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (262 ms)
55: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (530 ms total)
55:
55: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.434 0.217 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.767 3.547
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.466 0.234 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.329 7.210
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.445 0.223 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.490 6.877
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (759 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.485 0.243 199.9
55: (ns/day) (hour/ns)
55: Performance: 6.051 3.966
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.477 0.239 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.260 7.362
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.441 0.221 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.519 6.819
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (789 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.385 0.193 199.7
55: (ns/day) (hour/ns)
55: Performance: 7.624 3.148
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.379 0.190 199.4
55: (ns/day) (hour/ns)
55: Performance: 4.096 5.860
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.367 0.184 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.236 5.666
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (654 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.495 0.248 199.8
55: (ns/day) (hour/ns)
55: Performance: 5.929 4.048
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.428 0.214 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.629 6.614
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.458 0.229 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.393 7.074
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (792 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.435 0.218 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.746 3.558
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.417 0.209 199.5
55: (ns/day) (hour/ns)
55: Performance: 3.720 6.451
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.422 0.211 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.685 6.514
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (751 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.514 0.257 199.9
55: (ns/day) (hour/ns)
55: Performance: 5.717 4.198
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.332 0.166 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.676 5.133
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.333 0.167 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.661 5.149
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (680 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.444 0.722 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.033 11.805
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.924 0.463 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.681 14.278
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.964 0.482 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.612 14.884
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (1768 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.904 0.452 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.250 7.385
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.349 0.175 199.4
55: (ns/day) (hour/ns)
55: Performance: 4.445 5.399
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.416 0.208 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.737 6.423
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (933 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.485 0.243 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.049 3.968
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.437 0.219 199.2
55: (ns/day) (hour/ns)
55: Performance: 3.549 6.763
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.468 0.234 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.320 7.229
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (1055 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.484 0.243 199.6
55: (ns/day) (hour/ns)
55: Performance: 6.053 3.965
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.446 0.223 199.5
55: (ns/day) (hour/ns)
55: Performance: 3.480 6.897
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.430 0.216 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.607 6.653
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (1008 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.523 0.262 199.7
55: (ns/day) (hour/ns)
55: Performance: 5.611 4.277
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.560 0.280 199.5
55: (ns/day) (hour/ns)
55: Performance: 2.773 8.655
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.404 0.202 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.846 6.241
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (1330 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.466 0.233 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.297 3.811
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.372 0.187 199.3
55: (ns/day) (hour/ns)
55: Performance: 4.168 5.758
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.238 0.620 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.255 19.124
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (1576 ms)
55: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (12096 ms total)
55:
55: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.593 0.297 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.943 4.855
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.534 0.268 199.0
55: (ns/day) (hour/ns)
55: Performance: 2.898 8.280
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.641 0.321 199.7
55: (ns/day) (hour/ns)
55: Performance: 2.425 9.898
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (1445 ms)
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.627 0.313 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.686 5.122
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.603 0.302 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.575 9.319
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.547 0.274 199.7
55: (ns/day) (hour/ns)
55: Performance: 2.838 8.457
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (1179 ms)
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.545 0.273 199.7
55: (ns/day) (hour/ns)
55: Performance: 5.385 4.456
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.471 0.236 199.0
55: (ns/day) (hour/ns)
55: Performance: 3.288 7.299
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.976 0.489 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.592 15.080
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (1581 ms)
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.593 0.297 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.950 4.849
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.572 0.287 199.5
55: (ns/day) (hour/ns)
55: Performance: 2.713 8.847
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.556 0.279 199.7
55: (ns/day) (hour/ns)
55: Performance: 2.790 8.601
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (1337 ms)
55: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (5545 ms total)
55:
55: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.444 0.222 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.608 3.632
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.463 0.232 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.355 7.153
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.462 0.231 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.365 7.132
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (775 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.400 0.201 199.7
55: (ns/day) (hour/ns)
55: Performance: 7.325 3.276
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.417 0.209 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.724 6.444
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.479 0.240 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.243 7.401
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (744 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.369 0.185 199.7
55: (ns/day) (hour/ns)
55: Performance: 7.941 3.022
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.397 0.199 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.913 6.133
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.436 0.218 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.565 6.733
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (700 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.420 0.210 199.8
55: (ns/day) (hour/ns)
55: Performance: 6.981 3.438
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.462 0.231 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.363 7.137
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.456 0.228 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.404 7.050
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (766 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.506 0.253 199.8
55: (ns/day) (hour/ns)
55: Performance: 5.803 4.136
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.366 0.683 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.138 21.091
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.793 0.397 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.960 12.244
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (1432 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 2.690 1.345 200.0
55: (ns/day) (hour/ns)
55: Performance: 1.092 21.979
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.587 0.294 199.7
55: (ns/day) (hour/ns)
55: Performance: 2.644 9.077
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.439 0.220 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.537 6.786
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (1956 ms)
55: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (6377 ms total)
55:
55: [----------] 6 tests from NPH/MdrunNoAppendContinuationIsExact
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.434 0.217 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.754 3.553
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.351 0.176 199.5
55: (ns/day) (hour/ns)
55: Performance: 4.419 5.431
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.351 0.176 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.424 5.426
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (662 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.444 0.222 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.612 3.630
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.395 0.198 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.925 6.114
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.395 0.698 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.114 21.538
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (1211 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.776 0.388 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.782 6.346
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.418 0.209 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.717 6.456
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.662 0.331 199.8
55: (ns/day) (hour/ns)
55: Performance: 2.347 10.224
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (1021 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.265 0.633 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.321 10.342
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.528 0.265 199.7
55: (ns/day) (hour/ns)
55: Performance: 2.939 8.166
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.489 0.745 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.044 22.983
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (1733 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.539 0.270 199.9
55: (ns/day) (hour/ns)
55: Performance: 5.450 4.404
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.446 0.223 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.483 6.890
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.442 0.221 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.517 6.824
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (798 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.441 0.221 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.659 3.604
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.356 0.178 199.6
55: (ns/day) (hour/ns)
55: Performance: 4.359 5.506
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.377 0.189 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.122 5.822
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (698 ms)
55: [----------] 6 tests from NPH/MdrunNoAppendContinuationIsExact (6126 ms total)
55:
55: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.424 0.212 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.922 3.467
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.422 0.212 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.676 6.530
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.469 0.235 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.312 7.247
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (760 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.511 0.256 199.7
55: (ns/day) (hour/ns)
55: Performance: 5.747 4.176
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.445 0.223 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.492 6.874
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.465 0.233 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.338 7.190
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (802 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.607 0.304 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.831 4.967
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.378 0.689 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.128 21.277
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.681 0.841 199.9
55: (ns/day) (hour/ns)
55: Performance: 0.925 25.954
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (1927 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.421 0.211 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.971 3.443
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.420 0.210 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.700 6.487
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.468 0.234 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.322 7.224
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (753 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.446 0.223 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.577 3.649
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.531 0.266 199.5
55: (ns/day) (hour/ns)
55: Performance: 2.923 8.211
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.504 0.252 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.083 7.784
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (841 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.452 0.226 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.494 3.696
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.397 0.199 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.906 6.145
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.372 0.186 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.176 5.747
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (701 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55:
55: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Using Berendsen pressure coupling invalidates the true ensemble for the
55: thermostat
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: There was 1 warning
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55:
55: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Using Berendsen pressure coupling invalidates the true ensemble for the
55: thermostat
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: There was 1 warning
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.401 0.201 199.7
55: (ns/day) (hour/ns)
55: Performance: 7.320 3.279
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.410 0.206 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.784 6.343
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.390 0.195 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.978 6.033
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (701 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.413 0.207 199.7
55: (ns/day) (hour/ns)
55: Performance: 7.102 3.379
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.433 0.217 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.587 6.692
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.479 0.240 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.243 7.401
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (766 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.637 0.319 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.609 5.207
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.429 0.715 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.088 22.065
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.169 0.585 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.329 18.057
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (1721 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.479 0.240 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.120 3.921
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.411 0.206 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.780 6.349
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.368 0.184 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.220 5.688
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (733 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.458 0.229 199.8
55: (ns/day) (hour/ns)
55: Performance: 6.402 3.749
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.434 0.217 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.584 6.697
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.436 0.218 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.559 6.743
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (766 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.462 0.232 199.5
55: (ns/day) (hour/ns)
55: Performance: 6.338 3.787
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.439 0.220 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.540 6.780
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.127 0.564 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.379 17.405
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (1110 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.532 0.266 199.8
55: (ns/day) (hour/ns)
55: Performance: 5.519 4.348
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.417 0.209 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.725 6.443
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.394 0.198 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.937 6.097
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (767 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.466 0.233 199.8
55: (ns/day) (hour/ns)
55: Performance: 6.297 3.811
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.751 0.376 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.071 11.590
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 2.408 1.204 199.9
55: (ns/day) (hour/ns)
55: Performance: 0.646 37.165
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (1987 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.505 0.253 199.7
55: (ns/day) (hour/ns)
55: Performance: 5.812 4.129
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.351 0.676 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.150 20.871
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.455 0.228 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.412 7.034
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (1257 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15
55: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (0 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16
55: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (0 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.538 0.269 199.8
55: (ns/day) (hour/ns)
55: Performance: 5.453 4.401
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.389 0.195 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.993 6.010
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.412 0.206 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.769 6.367
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (798 ms)
55: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact (16400 ms total)
55:
55: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact
55: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.454 0.227 199.7
55: (ns/day) (hour/ns)
55: Performance: 6.464 3.713
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.389 0.195 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.993 6.011
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.399 0.200 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.895 6.162
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (717 ms)
55: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (717 ms total)
55:
55: [----------] 3 tests from Checking/InitialConstraintsTest
55: [ RUN ] Checking/InitialConstraintsTest.Works/0
55: Number of degrees of freedom in T-Coupling group rest is 11.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 1141.954 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc-and-methanol'
55: 1 steps, 0.0 ps.
55: Setting the LD random seed to -184682673
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.333 0.167 199.6
55: (ns/day) (hour/ns)
55: Performance: 1.035 23.199
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (204 ms)
55: [ RUN ] Checking/InitialConstraintsTest.Works/1
55: Number of degrees of freedom in T-Coupling group rest is 11.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 1141.954 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc-and-methanol'
55: 1 steps, 0.0 ps.
55: Setting the LD random seed to -1210267153
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.305 0.153 199.7
55: (ns/day) (hour/ns)
55: Performance: 1.132 21.199
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (189 ms)
55: [ RUN ] Checking/InitialConstraintsTest.Works/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
55: Integrator method md-vv-avek is implemented primarily for validation
55: purposes; for molecular dynamics, you should probably be using md or md-vv
55:
55: Number of degrees of freedom in T-Coupling group rest is 11.00
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
55: NVE simulation: will use the initial temperature of 1141.954 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc-and-methanol'
55: 1 steps, 0.0 ps.
55: Setting the LD random seed to -448790533
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.316 0.158 199.6
55: (ns/day) (hour/ns)
55: Performance: 1.091 22.005
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (198 ms)
55: [----------] 3 tests from Checking/InitialConstraintsTest (592 ms total)
55:
55: [----------] Global test environment tear-down
55: [==========] 61 tests from 10 test cases ran. (51263 ms total)
55: [ PASSED ] 61 tests.
55/65 Test #55: MdrunIOTests .......................... Passed 51.37 sec
test 56
Start 56: MdrunTests
56: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunTests.xml"
56: Test timeout computed to be: 600
56: [==========] Running 14 tests from 6 test cases.
56: [----------] Global test environment set-up.
56: [----------] 1 test from OriresTest
56: [ RUN ] OriresTest.OriresCanRun
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
56: The Berendsen thermostat does not generate the correct kinetic energy
56: distribution. You might want to consider using the V-rescale thermostat.
56:
56: Generating 1-4 interactions: fudge = 0.5
56: Number of degrees of freedom in T-Coupling group System is 518.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
56: You are using a plain Coulomb cut-off, which might produce artifacts.
56: You might want to consider using PME electrostatics.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
56: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank.
56: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164
56:
56:
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1'
56: 10 steps, 0.0 ps.
56: Setting the LD random seed to -8454210
56:
56: Generated 2145 of the 2145 non-bonded parameter combinations
56:
56: Generated 2145 of the 2145 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning H bonds into constraints...
56:
56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
56:
56: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm
56:
56: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm
56:
56: Note that mdrun will redetermine rlist based on the actual pair-list setup
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.559 0.280 199.7
56: (ns/day) (hour/ns)
56: Performance: 6.793 3.533
56: [ OK ] OriresTest.OriresCanRun (2514 ms)
56: [----------] 1 test from OriresTest (2515 ms total)
56:
56: [----------] 1 test from CompelTest
56: [ RUN ] CompelTest.SwapCanRun
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
56: The Berendsen thermostat does not generate the correct kinetic energy
56: distribution. You might want to consider using the V-rescale thermostat.
56:
56: Generating 1-4 interactions: fudge = 0.5
56: Split0 group 'Ch0' contains 83 atoms.
56: Split1 group 'Ch1' contains 83 atoms.
56: Solvent group 'SOL' contains 11931 atoms.
56: Swap group 'NA+' contains 19 atoms.
56: Swap group 'CL-' contains 19 atoms.
56: Number of degrees of freedom in T-Coupling group System is 27869.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
56: You are using a plain Coulomb cut-off, which might produce artifacts.
56: You might want to consider using PME electrostatics.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: SWAP: Determining initial numbers of ions per compartment.
56: SWAP: Setting pointers for checkpoint writing
56: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
56: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
56: starting mdrun 'Channel_coco in octane membrane'
56: 2 steps, 0.0 ps.
56: Setting the LD random seed to -170430721
56:
56: Generated 330891 of the 330891 non-bonded parameter combinations
56:
56: Generated 330891 of the 330891 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein'
56:
56: turning all bonds into constraints...
56:
56: Excluding 3 bonded neighbours molecule type 'OCT'
56:
56: turning all bonds into constraints...
56:
56: Excluding 1 bonded neighbours molecule type 'NA'
56:
56: turning all bonds into constraints...
56:
56: Excluding 1 bonded neighbours molecule type 'CL'
56:
56: turning all bonds into constraints...
56:
56: Excluding 3 bonded neighbours molecule type 'Protein'
56:
56: Excluding 3 bonded neighbours molecule type 'OCT'
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning all bonds into constraints...
56:
56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
56:
56: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
56:
56: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
56:
56: Note that mdrun will redetermine rlist based on the actual pair-list setup
56:
56: This run will generate roughly 1 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 6.720 3.361 200.0
56: (ns/day) (hour/ns)
56: Performance: 0.386 62.232
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
56: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
56:
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: SWAP: Setting pointers for checkpoint writing
56: SWAP: Copying channel fluxes from checkpoint file data
56: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
56: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
56: starting mdrun 'Channel_coco in octane membrane'
56: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 6.205 3.103 200.0
56: (ns/day) (hour/ns)
56: Performance: 0.418 57.467
56: [ OK ] CompelTest.SwapCanRun (12110 ms)
56: [----------] 1 test from CompelTest (12110 ms total)
56:
56: [----------] 6 tests from BondedInteractionsTest
56: [ RUN ] BondedInteractionsTest.NormalBondWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 2 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 183.9
56: (ns/day) (hour/ns)
56: Performance: 71.703 0.335
56: Setting the LD random seed to -1098940933
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.NormalBondWorks (51 ms)
56: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 2 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 184.2
56: (ns/day) (hour/ns)
56: Performance: 71.760 0.334
56: Setting the LD random seed to -134319172
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.TabulatedBondWorks (55 ms)
56: [ RUN ] BondedInteractionsTest.NormalAngleWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 183.9
56: (ns/day) (hour/ns)
56: Performance: 70.737 0.339
56: Setting the LD random seed to 612289493
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.NormalAngleWorks (32 ms)
56: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 184.8
56: (ns/day) (hour/ns)
56: Performance: 66.775 0.359
56: Setting the LD random seed to 1475264497
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (45 ms)
56: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 183.8
56: (ns/day) (hour/ns)
56: Performance: 71.196 0.337
56: Setting the LD random seed to 1274438895
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.NormalDihedralWorks (33 ms)
56: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.002 0.001 183.9
56: (ns/day) (hour/ns)
56: Performance: 71.043 0.338
56: Setting the LD random seed to -391152644
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (46 ms)
56: [----------] 6 tests from BondedInteractionsTest (263 ms total)
56:
56: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest
56: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0
56: Number of degrees of freedom in T-Coupling group rest is 10.00
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'Dipoles'
56: 20 steps, 0.1 ps.
56: Setting the LD random seed to -556798249
56:
56: Generated 1 of the 1 non-bonded parameter combinations
56:
56: Excluding 1 bonded neighbours molecule type 'Dipole'
56:
56: Searching the wall atom type(s)
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200
56:
56: Estimate for the relative computational load of the PME mesh part: 1.00
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.769 0.385 199.8
56: (ns/day) (hour/ns)
56: Performance: 11.783 2.037
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Last energy frame read 5 time 0.050 trr version: GMX_trn_file (double precision)
56:
56: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (555 ms)
56: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1
56: Test system 'epsilon-surface-constraint' cannot run with 1 ranks.
56: The supported numbers are > 1.
56: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (1 ms)
56: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: With epsilon_surface > 0 all molecules should be neutral.
56:
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: With epsilon_surface > 0 you can only use domain decomposition when there
56: are only small molecules with all bonds constrained (mdrun will check for
56: this).
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 4 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'Dipoles'
56: 20 steps, 0.1 ps.
56: Setting the LD random seed to -539050305
56:
56: Generated 1 of the 1 non-bonded parameter combinations
56:
56: Excluding 1 bonded neighbours molecule type 'Dipole'
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200
56:
56: Estimate for the relative computational load of the PME mesh part: 1.00
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.777 0.389 199.8
56: (ns/day) (hour/ns)
56: Performance: 11.660 2.058
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Last energy frame read 5 time 0.050
56: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (487 ms)
56: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (1043 ms total)
56:
56: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest
56: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -17121409
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.455 0.228 199.6
56: (ns/day) (hour/ns)
56: Performance: 1.897 12.653
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -1082737153
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.453 0.227 199.6
56: (ns/day) (hour/ns)
56: Performance: 1.903 12.612
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004
56:
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (800 ms)
56: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -1291847681
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.486 0.244 199.7
56: (ns/day) (hour/ns)
56: Performance: 1.773 13.537
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -135270930
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.362 0.181 199.5
56: (ns/day) (hour/ns)
56: Performance: 2.381 10.082
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004
56:
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (717 ms)
56: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (1517 ms total)
56:
56: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest
56: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0
56: Generating 1-4 interactions: fudge = 0.5
56: Pull group 1 'FirstWaterMolecule' has 3 atoms
56: Pull group 2 'SecondWaterMolecule' has 3 atoms
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56: Pull group natoms pbc atom distance at start reference at t=0
56: 1 3 2
56: 2 3 5 1.112 nm 1.000 nm
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting mdrun 'spc2'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -923209857
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Generated 3 of the 3 1-4 parameter combinations
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning H bonds into constraints...
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.458 0.230 199.6
56: (ns/day) (hour/ns)
56: Performance: 1.882 12.753
56: Generating 1-4 interactions: fudge = 0.5
56: Pull group 1 'FirstWaterMolecule' has 3 atoms
56: Pull group 2 'SecondWaterMolecule' has 3 atoms
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56: Pull group natoms pbc atom distance at start reference at t=0
56: 1 3 2
56: 2 3 5 1.112 nm 1.000 nm
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting mdrun 'spc2'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -67526737
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Generated 3 of the 3 1-4 parameter combinations
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning H bonds into constraints...
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.562 0.281 199.7
56: (ns/day) (hour/ns)
56: Performance: 1.535 15.634
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004
56:
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (606 ms)
56: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (606 ms total)
56:
56: [----------] Global test environment tear-down
56: [==========] 14 tests from 6 test cases ran. (18274 ms total)
56: [ PASSED ] 14 tests.
56/65 Test #56: MdrunTests ............................ Passed 18.36 sec
test 57
Start 57: MdrunPmeTests
57: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-pme-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunPmeTests.xml"
57: Test timeout computed to be: 600
57: [==========] Running 3 tests from 1 test case.
57: [----------] Global test environment set-up.
57: [----------] 3 tests from PmeTest
57: [ RUN ] PmeTest.ReproducesEnergies
57: Number of degrees of freedom in T-Coupling group rest is 12.00
57:
57: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
57: NVE simulation: will use the initial temperature of 1046.791 K for
57: determining the Verlet buffer size
57:
57:
57: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
57: The optimal PME mesh load for parallel simulations is below 0.5
57: and for highly parallel simulations between 0.25 and 0.33,
57: for higher performance, increase the cut-off and the PME grid spacing.
57:
57:
57:
57: There were 2 notes
57: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 20 steps, 0.0 ps.
57: Setting the LD random seed to -287310354
57:
57: Generated 8 of the 10 non-bonded parameter combinations
57:
57: Excluding 2 bonded neighbours molecule type 'Methanol'
57:
57: Excluding 2 bonded neighbours molecule type 'SOL'
57:
57: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
57:
57: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
57:
57: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
57:
57: Note that mdrun will redetermine rlist based on the actual pair-list setup
57: Calculating fourier grid dimensions for X Y Z
57: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
57:
57: Estimate for the relative computational load of the PME mesh part: 1.00
57:
57: This run will generate roughly 0 Mb of data
57:
57: Writing final coordinates.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.692 0.346 199.8
57: (ns/day) (hour/ns)
57: Performance: 5.243 4.577
57: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
57:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 20 steps, 0.0 ps.
57:
57: Writing final coordinates.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.662 0.331 199.8
57: (ns/day) (hour/ns)
57: Performance: 5.475 4.383
57: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
57:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57:
57: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
57: starting mdrun 'spc-and-methanol'
57: 20 steps, 0.0 ps.
57:
57: Writing final coordinates.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.708 0.354 199.8
57: (ns/day) (hour/ns)
57: Performance: 5.119 4.689
57: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
57:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (1240 ms)
57: [ RUN ] PmeTest.ScalesTheBox
57:
57: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
57: For a correct single-point energy evaluation with nsteps = 0, use
57: continuation = yes to avoid constraining the input coordinates.
57:
57: Number of degrees of freedom in T-Coupling group rest is 12.00
57:
57: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
57: NVE simulation: will use the initial temperature of 1046.791 K for
57: determining the Verlet buffer size
57:
57:
57: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
57: The optimal PME mesh load for parallel simulations is below 0.5
57: and for highly parallel simulations between 0.25 and 0.33,
57: for higher performance, increase the cut-off and the PME grid spacing.
57:
57:
57:
57: There were 3 notes
57: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 0 steps, 0.0 ps.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.018 0.010 191.6
57: (ns/day) (hour/ns)
57: Performance: 8.968 2.676
57: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
57:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -541361541
57:
57: Generated 8 of the 10 non-bonded parameter combinations
57:
57: Excluding 2 bonded neighbours molecule type 'Methanol'
57:
57: Excluding 2 bonded neighbours molecule type 'SOL'
57:
57: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
57:
57: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
57:
57: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
57:
57: Note that mdrun will redetermine rlist based on the actual pair-list setup
57: Calculating fourier grid dimensions for X Y Z
57: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
57:
57: Estimate for the relative computational load of the PME mesh part: 1.00
57:
57: This run will generate roughly 0 Mb of data
57: [ OK ] PmeTest.ScalesTheBox (111 ms)
57: [ RUN ] PmeTest.ScalesTheBoxWithWalls
57:
57: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
57: For a correct single-point energy evaluation with nsteps = 0, use
57: continuation = yes to avoid constraining the input coordinates.
57:
57: Number of degrees of freedom in T-Coupling group rest is 13.00
57:
57: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
57: NVE simulation: will use the initial temperature of 966.268 K for
57: determining the Verlet buffer size
57:
57:
57: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
57: The optimal PME mesh load for parallel simulations is below 0.5
57: and for highly parallel simulations between 0.25 and 0.33,
57: for higher performance, increase the cut-off and the PME grid spacing.
57:
57:
57:
57: There were 3 notes
57: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 0 steps, 0.0 ps.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.096 0.049 198.3
57: (ns/day) (hour/ns)
57: Performance: 1.776 13.512
57: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
57:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -537959553
57:
57: Generated 8 of the 10 non-bonded parameter combinations
57:
57: Excluding 2 bonded neighbours molecule type 'Methanol'
57:
57: Excluding 2 bonded neighbours molecule type 'SOL'
57:
57: Searching the wall atom type(s)
57:
57: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
57:
57: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
57:
57: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
57:
57: Note that mdrun will redetermine rlist based on the actual pair-list setup
57: Calculating fourier grid dimensions for X Y Z
57: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
57:
57: Estimate for the relative computational load of the PME mesh part: 1.00
57:
57: This run will generate roughly 0 Mb of data
57: [ OK ] PmeTest.ScalesTheBoxWithWalls (234 ms)
57: [----------] 3 tests from PmeTest (1586 ms total)
57:
57: [----------] Global test environment tear-down
57: [==========] 3 tests from 1 test case ran. (1625 ms total)
57: [ PASSED ] 3 tests.
57/65 Test #57: MdrunPmeTests ......................... Passed 1.70 sec
test 58
Start 58: MdrunNonIntegratorTests
58: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml"
58: Test timeout computed to be: 600
58: [==========] Running 65 tests from 7 test cases.
58: [----------] Global test environment set-up.
58: [----------] 1 test from NonbondedBenchTest
58: [ RUN ] NonbondedBenchTest.BasicEndToEndTest
58: System size: 3000 atoms
58: Cut-off radius: 1 nm
58: Number of threads: 1
58: Number of iterations: 1
58: Compute energies: no
58: Ewald excl. corr.: analytical
58:
58: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle
58: total useful
58: Ewald all geom. no 0.000 0.0000 inf inf
58: [ OK ] NonbondedBenchTest.BasicEndToEndTest (749 ms)
58: [----------] 1 test from NonbondedBenchTest (750 ms total)
58:
58: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -4.79910463671070e+01
58: Maximum force = 1.86297359432219e+02 on atom 13
58: Norm of force = 8.77219865482161e+01
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (4048 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 3.02331e+02 on atom 3
58: F-Norm = 1.18024e+02
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -5.58622538633290e+01
58: Maximum force = 4.27274822366527e+02 on atom 13
58: Norm of force = 1.84530029253829e+02
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (4018 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 22.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 3.19376899751521e+02
58: Maximum force = 9.99884921009767e+03 on atom 9
58: Norm of force = 4.61669565054298e+03
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: turning H bonds into constraints...
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (996 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58:
58: NOTE 3 [file glycine_vacuo.top, line 12]:
58: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
58:
58: Number of degrees of freedom in T-Coupling group System is 22.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 2.41575e+04 on atom 10
58: F-Norm = 1.18451e+04
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 1.51743018140925e+02
58: Maximum force = 7.42089573409111e+03 on atom 9
58: Norm of force = 3.56929298615739e+03
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: turning H bonds into constraints...
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (997 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -1.56984193848276e+02
58: Maximum force = 4.56923624626296e+02 on atom 17
58: Norm of force = 1.83258377168331e+02
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (121 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58:
58: NOTE 4 [file unknown]:
58: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 5 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 1.06800e+03 on atom 28
58: F-Norm = 4.26922e+02
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -1.69410778678185e+02
58: Maximum force = 2.18225948473957e+02 on atom 17
58: Norm of force = 7.92068036537697e+01
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (123 ms)
58: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (10304 ms total)
58:
58: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents converged to Fmax < 10 in 1 steps
58: Potential Energy = -9.74257075835450e-01
58: Maximum force = 4.01322929015108e+00 on atom 1
58: Norm of force = 1.63839399694368e+00
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (39 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 4.01323e+00 on atom 1
58: F-Norm = 1.63839e+00
58:
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
58: Potential Energy = -9.90642313893957e-01
58: Maximum force = 2.57812909491105e+00 on atom 1
58: Norm of force = 1.05251679559258e+00
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (38 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58:
58: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58:
58: There was 1 warning
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Low-Memory BFGS Minimizer:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: Using 10 BFGS correction steps.
58:
58: F-max = 4.01323e+00 on atom 1
58: F-Norm = 1.63839e+00
58:
58:
58: writing lowest energy coordinates.
58:
58: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
58: Potential Energy = -9.90642313893957e-01
58: Maximum force = 2.57812909491105e+00 on atom 1
58: Norm of force = 1.05251679559258e+00
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (36 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 3.19395484891517e+02
58: Maximum force = 9.97041707197910e+03 on atom 9
58: Norm of force = 4.62274878665467e+03
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (1005 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 2.41672e+04 on atom 10
58: F-Norm = 1.19357e+04
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 1.56258793899479e+02
58: Maximum force = 7.50181017480397e+03 on atom 9
58: Norm of force = 3.61390332564874e+03
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (1135 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58:
58: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58:
58: There was 1 warning
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Low-Memory BFGS Minimizer:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: Using 10 BFGS correction steps.
58:
58: F-max = 2.41672e+04 on atom 10
58: F-Norm = 1.19357e+04
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 5.61116097794203e+02
58: Maximum force = 1.26854826291223e+04 on atom 10
58: Norm of force = 6.06436286976271e+03
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (1314 ms)
58: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (3569 ms total)
58:
58: [----------] 5 tests from NormalModesWorks/NormalModesTest
58: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 15.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Small system size (N=6), using full Hessian format.
58: Allocating Hessian memory...
58:
58: starting normal mode calculation '2 scaled waters'
58: 12 steps.
58:
58: Maximum force: 9.96989e-06
58:
58:
58: Writing Hessian...
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Reading double precision matrix generated by GROMACS 2021.3-Raspbian-2021.3-4
58:
58: Diagonalizing to find vectors 7 through 18...
58: Writing eigenvalues...
58:
58: Writing average structure & eigenvectors 7--18 to eigenvec.trr
58: Generated 3 of the 3 non-bonded parameter combinations
58:
58: Generated 3 of the 3 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: This run will generate roughly 0 Mb of data
58: There are: 6 Atoms
58: Using begin = 7 and end = 18
58: Full matrix storage format, nrow=18, ncols=18
58: Writing eigenfrequencies - negative eigenvalues will be set to zero.
58: Cannot compute entropy when -first = 7
58: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (98 ms)
58: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58:
58: NOTE 3 [file villin.top, line 2452]:
58: System has non-zero total charge: -2.000000
58: Total charge should normally be an integer. See
58: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
58: for discussion on how close it should be to an integer.
58:
58:
58:
58: Number of degrees of freedom in T-Coupling group System is 765.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Small system size (N=256), using full Hessian format.
58: Allocating Hessian memory...
58:
58: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN'
58: 512 steps.
58:
58: Maximum force: 6.97568e-04
58:
58:
58: Writing Hessian...
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Reading double precision matrix generated by GROMACS 2021.3-Raspbian-2021.3-4
58:
58: Diagonalizing to find vectors 7 through 50...
58: Writing eigenvalues...
58:
58: Writing average structure & eigenvectors 7--50 to eigenvec.trr
58: Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
58:
58: This run will generate roughly 0 Mb of data
58: There are: 256 Atoms
58: Using begin = 7 and end = 50
58: Full matrix storage format, nrow=768, ncols=768
58: Writing eigenfrequencies - negative eigenvalues will be set to zero.
58: Cannot compute entropy when -first = 7
58: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (22854 ms)
58: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 15.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Small system size (N=6), using full Hessian format.
58: Allocating Hessian memory...
58:
58: starting normal mode calculation 'flex spc dimer'
58: 12 steps.
58:
58: Maximum force: 3.36401e-04
58:
58:
58: Writing Hessian...
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Reading double precision matrix generated by GROMACS 2021.3-Raspbian-2021.3-4
58:
58: Diagonalizing to find vectors 7 through 18...
58: Writing eigenvalues...
58:
58: Writing average structure & eigenvectors 7--18 to eigenvec.trr
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: This run will generate roughly 0 Mb of data
58: There are: 6 Atoms
58: Using begin = 7 and end = 18
58: Full matrix storage format, nrow=18, ncols=18
58: Writing eigenfrequencies - negative eigenvalues will be set to zero.
58: Cannot compute entropy when -first = 7
58: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (4401 ms)
58: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 6.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Small system size (N=3), using full Hessian format.
58: Allocating Hessian memory...
58:
58: starting normal mode calculation '1 TIP5P'
58: 6 steps.
58:
58: Maximum force: 2.42882e-04
58:
58:
58: Writing Hessian...
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Reading double precision matrix generated by GROMACS 2021.3-Raspbian-2021.3-4
58:
58: Diagonalizing to find vectors 7 through 9...
58: Writing eigenvalues...
58:
58: Writing average structure & eigenvectors 7--9 to eigenvec.trr
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: This run will generate roughly 0 Mb of data
58: There are: 3 Atoms
58: There are: 2 VSites
58: Using begin = 7 and end = 9
58: Full matrix storage format, nrow=9, ncols=9
58: Writing eigenfrequencies - negative eigenvalues will be set to zero.
58: Cannot compute entropy when -first = 7
58: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (4276 ms)
58: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58: Number of degrees of freedom in T-Coupling group System is 15.00
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Small system size (N=6), using full Hessian format.
58: Allocating Hessian memory...
58:
58: starting normal mode calculation 'sw dimer'
58: 12 steps.
58:
58: Maximum force: 1.07599e-03
58: The force is probably not small enough to ensure that you are at a minimum.
58: Be aware that negative eigenvalues may occur
58: when the resulting matrix is diagonalized.
58:
58:
58: Writing Hessian...
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Reading double precision matrix generated by GROMACS 2021.3-Raspbian-2021.3-4
58:
58: Diagonalizing to find vectors 7 through 18...
58: Writing eigenvalues...
58:
58: Writing average structure & eigenvectors 7--18 to eigenvec.trr
58: Generated 6 of the 10 non-bonded parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SW'
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: This run will generate roughly 0 Mb of data
58: There are: 6 Atoms
58: There are: 2 Shells
58: There are: 2 VSites
58:
58: NOTE: in the current version shell prediction during the crun is disabled
58:
58: Using begin = 7 and end = 18
58: Full matrix storage format, nrow=18, ncols=18
58: Writing eigenfrequencies - negative eigenvalues will be set to zero.
58: Cannot compute entropy when -first = 7
58: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (78 ms)
58: [----------] 5 tests from NormalModesWorks/NormalModesTest (31715 ms total)
58:
58: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
58: NVE simulation: will use the initial temperature of 68.810 K for
58: determining the Verlet buffer size
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.411 0.206 199.7
58: (ns/day) (hour/ns)
58: Performance: 7.138 3.362
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr'
58:
58: trr version: GMX_trn_file (double precision)
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.007 0.004 193.8
58: (ns/day) (hour/ns)
58: Performance: 417.894 0.057
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (263 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
58: NVE simulation: will use the initial temperature of 68.810 K for
58: determining the Verlet buffer size
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.531 0.266 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.525 4.344
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.007 0.003 193.9
58: (ns/day) (hour/ns)
58: Performance: 425.544 0.056
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (323 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.413 0.207 199.8
58: (ns/day) (hour/ns)
58: Performance: 7.110 3.376
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.015 0.007 197.1
58: (ns/day) (hour/ns)
58: Performance: 196.548 0.122
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (309 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.399 0.200 199.8
58: (ns/day) (hour/ns)
58: Performance: 7.358 3.262
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.007 0.004 189.0
58: (ns/day) (hour/ns)
58: Performance: 417.469 0.057
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (257 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: NVE simulation: will use the initial temperature of 398.997 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.389 0.195 199.7
58: (ns/day) (hour/ns)
58: Performance: 7.530 3.187
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 193.8
58: (ns/day) (hour/ns)
58: Performance: 378.834 0.063
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (4536 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: NVE simulation: will use the initial temperature of 398.997 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.544 0.272 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.402 4.443
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 194.0
58: (ns/day) (hour/ns)
58: Performance: 374.755 0.064
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (4578 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.479 0.240 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.121 3.921
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 194.2
58: (ns/day) (hour/ns)
58: Performance: 374.937 0.064
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (4601 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.443 0.222 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.625 3.623
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 193.9
58: (ns/day) (hour/ns)
58: Performance: 376.242 0.064
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (4520 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: NVE simulation: will use the initial temperature of 456.887 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 6 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.492 0.246 199.7
58: (ns/day) (hour/ns)
58: Performance: 5.965 4.024
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.013 0.007 195.4
58: (ns/day) (hour/ns)
58: Performance: 224.847 0.107
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (418 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: NVE simulation: will use the initial temperature of 456.887 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 6 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.475 0.238 199.6
58: (ns/day) (hour/ns)
58: Performance: 6.173 3.888
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.014 0.007 195.7
58: (ns/day) (hour/ns)
58: Performance: 209.672 0.114
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (409 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 5 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.482 0.241 199.6
58: (ns/day) (hour/ns)
58: Performance: 6.086 3.944
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.014 0.007 195.6
58: (ns/day) (hour/ns)
58: Performance: 208.241 0.115
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (563 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 5 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.534 0.267 199.7
58: (ns/day) (hour/ns)
58: Performance: 5.496 4.367
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.014 0.007 195.8
58: (ns/day) (hour/ns)
58: Performance: 207.246 0.116
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (541 ms)
58: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (21321 ms total)
58:
58: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.628 0.314 199.7
58: (ns/day) (hour/ns)
58: Performance: 4.672 5.137
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.016 0.009 190.4
58: (ns/day) (hour/ns)
58: Performance: 172.575 0.139
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (486 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.518 0.260 199.6
58: (ns/day) (hour/ns)
58: Performance: 5.657 4.242
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.016 0.008 190.3
58: (ns/day) (hour/ns)
58: Performance: 174.062 0.138
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (433 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.583 0.292 199.6
58: (ns/day) (hour/ns)
58: Performance: 5.027 4.774
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.018 0.009 190.1
58: (ns/day) (hour/ns)
58: Performance: 156.000 0.154
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (479 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.532 0.267 199.7
58: (ns/day) (hour/ns)
58: Performance: 5.509 4.356
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 187.5
58: (ns/day) (hour/ns)
58: Performance: 163.454 0.147
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (445 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.510 0.255 199.6
58: (ns/day) (hour/ns)
58: Performance: 5.751 4.173
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 188.6
58: (ns/day) (hour/ns)
58: Performance: 163.026 0.147
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (434 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.680 0.341 199.7
58: (ns/day) (hour/ns)
58: Performance: 4.312 5.565
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 188.9
58: (ns/day) (hour/ns)
58: Performance: 162.763 0.147
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (545 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.574 0.287 199.7
58: (ns/day) (hour/ns)
58: Performance: 5.113 4.694
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 188.6
58: (ns/day) (hour/ns)
58: Performance: 163.112 0.147
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (466 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.593 0.297 199.7
58: (ns/day) (hour/ns)
58: Performance: 4.948 4.850
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.018 0.009 189.4
58: (ns/day) (hour/ns)
58: Performance: 155.992 0.154
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (479 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.632 0.316 199.7
58: (ns/day) (hour/ns)
58: Performance: 4.642 5.170
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 189.3
58: (ns/day) (hour/ns)
58: Performance: 160.721 0.149
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (502 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.560 0.280 199.7
58: (ns/day) (hour/ns)
58: Performance: 5.238 4.582
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 189.3
58: (ns/day) (hour/ns)
58: Performance: 160.801 0.149
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (463 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.522 0.261 199.6
58: (ns/day) (hour/ns)
58: Performance: 5.617 4.273
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 190.1
58: (ns/day) (hour/ns)
58: Performance: 159.795 0.150
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (447 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.564 0.282 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.207 4.609
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 189.7
58: (ns/day) (hour/ns)
58: Performance: 163.602 0.147
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (462 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.597 0.299 199.9
58: (ns/day) (hour/ns)
58: Performance: 4.921 4.878
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 187.7
58: (ns/day) (hour/ns)
58: Performance: 163.022 0.147
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (477 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.578 0.289 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.080 4.724
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.016 0.009 188.2
58: (ns/day) (hour/ns)
58: Performance: 170.385 0.141
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (465 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.602 0.301 199.9
58: (ns/day) (hour/ns)
58: Performance: 4.874 4.924
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 188.6
58: (ns/day) (hour/ns)
58: Performance: 163.459 0.147
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (478 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.640 0.320 199.9
58: (ns/day) (hour/ns)
58: Performance: 4.586 5.234
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 188.7
58: (ns/day) (hour/ns)
58: Performance: 162.159 0.148
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (500 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.617 0.308 199.9
58: (ns/day) (hour/ns)
58: Performance: 4.762 5.040
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 188.3
58: (ns/day) (hour/ns)
58: Performance: 166.125 0.144
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (484 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.766 0.383 199.9
58: (ns/day) (hour/ns)
58: Performance: 3.834 6.260
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.016 0.009 188.2
58: (ns/day) (hour/ns)
58: Performance: 171.504 0.140
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (557 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.608 0.304 199.9
58: (ns/day) (hour/ns)
58: Performance: 4.829 4.970
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 188.6
58: (ns/day) (hour/ns)
58: Performance: 160.161 0.150
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (480 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.750 0.375 199.9
58: (ns/day) (hour/ns)
58: Performance: 3.915 6.131
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 188.7
58: (ns/day) (hour/ns)
58: Performance: 161.802 0.148
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (557 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.622 0.311 199.9
58: (ns/day) (hour/ns)
58: Performance: 4.722 5.083
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 188.7
58: (ns/day) (hour/ns)
58: Performance: 161.049 0.149
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (492 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.611 0.305 199.9
58: (ns/day) (hour/ns)
58: Performance: 4.809 4.991
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.056 0.028 196.4
58: (ns/day) (hour/ns)
58: Performance: 51.786 0.463
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (519 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.506 0.254 199.7
58: (ns/day) (hour/ns)
58: Performance: 5.793 4.143
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.016 0.009 189.3
58: (ns/day) (hour/ns)
58: Performance: 172.580 0.139
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (612 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.460 0.231 199.6
58: (ns/day) (hour/ns)
58: Performance: 6.371 3.767
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.016 0.008 190.3
58: (ns/day) (hour/ns)
58: Performance: 173.377 0.138
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (511 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.771 0.386 199.8
58: (ns/day) (hour/ns)
58: Performance: 3.807 6.304
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 188.9
58: (ns/day) (hour/ns)
58: Performance: 158.819 0.151
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (667 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 2.134 1.067 199.9
58: (ns/day) (hour/ns)
58: Performance: 1.376 17.439
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 188.9
58: (ns/day) (hour/ns)
58: Performance: 160.186 0.150
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (1350 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 1.312 0.656 199.9
58: (ns/day) (hour/ns)
58: Performance: 2.238 10.725
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.016 0.009 188.1
58: (ns/day) (hour/ns)
58: Performance: 171.223 0.140
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (963 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.639 0.320 199.7
58: (ns/day) (hour/ns)
58: Performance: 4.593 5.225
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.016 0.009 188.0
58: (ns/day) (hour/ns)
58: Performance: 170.093 0.141
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (613 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.563 0.282 199.7
58: (ns/day) (hour/ns)
58: Performance: 5.212 4.605
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.018 0.009 188.9
58: (ns/day) (hour/ns)
58: Performance: 155.941 0.154
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (566 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 1.363 0.682 199.9
58: (ns/day) (hour/ns)
58: Performance: 2.153 11.146
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.016 0.009 188.3
58: (ns/day) (hour/ns)
58: Performance: 170.687 0.141
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (968 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.516 0.258 199.7
58: (ns/day) (hour/ns)
58: Performance: 5.685 4.221
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 188.9
58: (ns/day) (hour/ns)
58: Performance: 160.224 0.150
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (542 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.536 0.268 199.7
58: (ns/day) (hour/ns)
58: Performance: 5.476 4.383
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 188.8
58: (ns/day) (hour/ns)
58: Performance: 160.578 0.149
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (556 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.596 0.298 199.7
58: (ns/day) (hour/ns)
58: Performance: 4.923 4.875
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.017 0.009 189.2
58: (ns/day) (hour/ns)
58: Performance: 160.299 0.150
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (590 ms)
58: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (18601 ms total)
58:
58: [----------] 2 tests from Angles1/SimpleMdrunTest
58: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file angles1.top, line 72]:
58: In moleculetype 'butane' 4 atoms are not bound by a potential or
58: constraint to any other atom in the same moleculetype. Although
58: technically this might not cause issues in a simulation, this often means
58: that the user forgot to add a bond/potential/constraint or put multiple
58: molecules in the same moleculetype definition by mistake. Run with -v to
58: get information for each atom.
58:
58: Number of degrees of freedom in T-Coupling group System is 9.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]:
58: NVE simulation: will use the initial temperature of 238.919 K for
58: determining the Verlet buffer size
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'This_incredible_box_of_butane'
58: 50 steps, 0.1 ps.
58: Generated 3 of the 3 non-bonded parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'butane'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.472 0.236 199.7
58: (ns/day) (hour/ns)
58: Performance: 18.655 1.287
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 5 time 0.020
Reading energy frame 6 time 0.024
Reading energy frame 7 time 0.028
Reading energy frame 8 time 0.032
Reading energy frame 9 time 0.036
Reading energy frame 10 time 0.040
Reading energy frame 11 time 0.044
Reading energy frame 12 time 0.048
Reading energy frame 13 time 0.050
Last energy frame read 13 time 0.050
58: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (301 ms)
58: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file angles1.top, line 72]:
58: In moleculetype 'butane' 4 atoms are not bound by a potential or
58: constraint to any other atom in the same moleculetype. Although
58: technically this might not cause issues in a simulation, this often means
58: that the user forgot to add a bond/potential/constraint or put multiple
58: molecules in the same moleculetype definition by mistake. Run with -v to
58: get information for each atom.
58:
58: Number of degrees of freedom in T-Coupling group System is 9.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]:
58: NVE simulation: will use the initial temperature of 238.919 K for
58: determining the Verlet buffer size
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'This_incredible_box_of_butane'
58: 50 steps, 0.1 ps.
58: Generated 3 of the 3 non-bonded parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'butane'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.494 0.247 199.9
58: (ns/day) (hour/ns)
58: Performance: 17.820 1.347
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 5 time 0.020
Reading energy frame 6 time 0.024
Reading energy frame 7 time 0.028
Reading energy frame 8 time 0.032
Reading energy frame 9 time 0.036
Reading energy frame 10 time 0.040
Reading energy frame 11 time 0.044
Reading energy frame 12 time 0.048
Reading energy frame 13 time 0.050
Last energy frame read 13 time 0.050
58: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (299 ms)
58: [----------] 2 tests from Angles1/SimpleMdrunTest (602 ms total)
58:
58: [----------] Global test environment tear-down
58: [==========] 65 tests from 7 test cases ran. (87090 ms total)
58: [ PASSED ] 65 tests.
58/65 Test #58: MdrunNonIntegratorTests ............... Passed 87.28 sec
test 59
Start 59: MdrunTpiTests
59: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml"
59: Test timeout computed to be: 600
59: [==========] Running 2 tests from 1 test case.
59: [----------] Global test environment set-up.
59: [----------] 2 tests from Simple/TpiTest
59: [ RUN ] Simple/TpiTest.ReproducesOutput/0
59: Ignoring obsolete mdp entry 'ns_type'
59: Generating 1-4 interactions: fudge = 0.5
59: Number of degrees of freedom in T-Coupling group System is 1308.00
59: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
59: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
59: TPI is not implemented for GPUs.
59:
59: Using 1 MPI thread
59: Using 1 OpenMP thread
59:
59:
59: NOTE: Thread affinity was not set.
59:
59: WARNING: Using the slow plain C kernels. This should
59: not happen during routine usage on supported platforms.
59: Reading frames from gro file '216 water molecules', 648 atoms.
59:
Reading frame 0 time 0.000 mu 8.706e+02 <mu> 8.706e+02
59:
Last frame 0 time 0.000
59: Generated 331705 of the 331705 non-bonded parameter combinations
59:
59: Generated 331705 of the 331705 1-4 parameter combinations
59:
59: Excluding 2 bonded neighbours molecule type 'SOL'
59:
59: Excluding 3 bonded neighbours molecule type 'methane'
59: Analysing residue names:
59: There are: 216 Water residues
59: There are: 1 Other residues
59: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
59:
59: This run will generate roughly 0 Mb of data
59: [ OK ] Simple/TpiTest.ReproducesOutput/0 (4955 ms)
59: [ RUN ] Simple/TpiTest.ReproducesOutput/1
59: Ignoring obsolete mdp entry 'ns_type'
59: Generating 1-4 interactions: fudge = 0.5
59: Number of degrees of freedom in T-Coupling group System is 1308.00
59: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
59: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
59: TPI is not implemented for GPUs.
59:
59: Using 1 MPI thread
59: Using 1 OpenMP thread
59:
59:
59: NOTE: Thread affinity was not set.
59:
59: WARNING: Using the slow plain C kernels. This should
59: not happen during routine usage on supported platforms.
59: Reading frames from gro file '216 water molecules', 648 atoms.
59:
Reading frame 0 time 0.000 mu 9.144e+01 <mu> 9.144e+01
59:
Last frame 0 time 0.000
59: Generated 331705 of the 331705 non-bonded parameter combinations
59:
59: Generated 331705 of the 331705 1-4 parameter combinations
59:
59: Excluding 2 bonded neighbours molecule type 'SOL'
59:
59: Excluding 3 bonded neighbours molecule type 'methane'
59: Analysing residue names:
59: There are: 216 Water residues
59: There are: 1 Other residues
59: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
59:
59: This run will generate roughly 0 Mb of data
59: [ OK ] Simple/TpiTest.ReproducesOutput/1 (4858 ms)
59: [----------] 2 tests from Simple/TpiTest (9813 ms total)
59:
59: [----------] Global test environment tear-down
59: [==========] 2 tests from 1 test case ran. (9852 ms total)
59: [ PASSED ] 2 tests.
59/65 Test #59: MdrunTpiTests ......................... Passed 9.93 sec
test 60
Start 60: MdrunMpiTests
60: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml"
60: Test timeout computed to be: 600
60: [==========] Running 22 tests from 7 test cases.
60: [----------] Global test environment set-up.
60: [----------] 1 test from DomainDecompositionSpecialCasesTest
60: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 9.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc2'
60: 0 steps, 0.0 ps.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.007 0.002 319.7
60: (ns/day) (hour/ns)
60: Performance: 41.919 0.573
60: Setting the LD random seed to -92443401
60:
60: Generated 3 of the 3 non-bonded parameter combinations
60:
60: Generated 3 of the 3 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (47 ms)
60: [----------] 1 test from DomainDecompositionSpecialCasesTest (47 ms total)
60:
60: [----------] 4 tests from MimicTest
60: [ RUN ] MimicTest.OneQuantumMol
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 21.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
60:
60: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 2.560 0.670 382.1
60: (ns/day) (hour/ns)
60: Performance: 0.129 186.087
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 1071509722
60:
60: Generated 10 of the 10 non-bonded parameter combinations
60:
60: Generated 10 of the 10 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.OneQuantumMol (2064 ms)
60: [ RUN ] MimicTest.AllQuantumMol
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 21.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
60:
60: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 2.540 0.665 382.0
60: (ns/day) (hour/ns)
60: Performance: 0.130 184.713
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 1605222295
60:
60: Generated 10 of the 10 non-bonded parameter combinations
60:
60: Generated 10 of the 10 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.AllQuantumMol (2042 ms)
60: [ RUN ] MimicTest.TwoQuantumMol
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 21.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
60:
60: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 2.600 0.680 382.4
60: (ns/day) (hour/ns)
60: Performance: 0.127 188.880
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -957682009
60:
60: Generated 10 of the 10 non-bonded parameter combinations
60:
60: Generated 10 of the 10 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.TwoQuantumMol (2083 ms)
60: [ RUN ] MimicTest.BondCuts
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 66.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
60: NVE simulation: will use the initial temperature of 300.368 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
60:
60: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 2.500 0.655 381.7
60: (ns/day) (hour/ns)
60: Performance: 0.132 181.936
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -173162515
60:
60: Generated 2211 of the 2211 non-bonded parameter combinations
60:
60: Generated 2211 of the 2211 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.BondCuts (2097 ms)
60: [----------] 4 tests from MimicTest (8286 ms total)
60:
60: [----------] 1 test from MultiSimTerminationTest
60: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
60: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
60: [----------] 1 test from MultiSimTerminationTest (0 ms total)
60:
60: [----------] 1 test from ReplicaExchangeTerminationTest
60: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
60: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
60: [----------] 1 test from ReplicaExchangeTerminationTest (1 ms total)
60:
60: [----------] 3 tests from PmeTest
60: [ RUN ] PmeTest.ReproducesEnergies
60: Number of degrees of freedom in T-Coupling group rest is 12.00
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
60: NVE simulation: will use the initial temperature of 1046.791 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
60: The optimal PME mesh load for parallel simulations is below 0.5
60: and for highly parallel simulations between 0.25 and 0.33,
60: for higher performance, increase the cut-off and the PME grid spacing.
60:
60:
60:
60: There were 2 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 20 steps, 0.0 ps.
60: Setting the LD random seed to 2084561855
60:
60: Generated 8 of the 10 non-bonded parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'Methanol'
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60: Calculating fourier grid dimensions for X Y Z
60: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
60:
60: Estimate for the relative computational load of the PME mesh part: 1.00
60:
60: This run will generate roughly 0 Mb of data
60:
60: Writing final coordinates.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 8.900 2.265 393.0
60: (ns/day) (hour/ns)
60: Performance: 0.801 29.958
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 20 steps, 0.0 ps.
60:
60: Writing final coordinates.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 8.974 2.282 393.2
60: (ns/day) (hour/ns)
60: Performance: 0.795 30.189
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
60: starting mdrun 'spc-and-methanol'
60: 20 steps, 0.0 ps.
60:
60: Writing final coordinates.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 9.107 2.310 394.3
60: (ns/day) (hour/ns)
60: Performance: 0.786 30.552
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (9762 ms)
60: [ RUN ] PmeTest.ScalesTheBox
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Number of degrees of freedom in T-Coupling group rest is 12.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
60: NVE simulation: will use the initial temperature of 1046.791 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
60: The optimal PME mesh load for parallel simulations is below 0.5
60: and for highly parallel simulations between 0.25 and 0.33,
60: for higher performance, increase the cut-off and the PME grid spacing.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 0 steps, 0.0 ps.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.411 0.142 288.6
60: (ns/day) (hour/ns)
60: Performance: 0.607 39.531
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -67110539
60:
60: Generated 8 of the 10 non-bonded parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'Methanol'
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60: Calculating fourier grid dimensions for X Y Z
60: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
60:
60: Estimate for the relative computational load of the PME mesh part: 1.00
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] PmeTest.ScalesTheBox (1107 ms)
60: [ RUN ] PmeTest.ScalesTheBoxWithWalls
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Number of degrees of freedom in T-Coupling group rest is 13.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
60: NVE simulation: will use the initial temperature of 966.268 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
60: The optimal PME mesh load for parallel simulations is below 0.5
60: and for highly parallel simulations between 0.25 and 0.33,
60: for higher performance, increase the cut-off and the PME grid spacing.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 0 steps, 0.0 ps.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.861 0.255 337.8
60: (ns/day) (hour/ns)
60: Performance: 0.339 70.778
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 2137825279
60:
60: Generated 8 of the 10 non-bonded parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'Methanol'
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: Searching the wall atom type(s)
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60: Calculating fourier grid dimensions for X Y Z
60: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
60:
60: Estimate for the relative computational load of the PME mesh part: 1.00
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] PmeTest.ScalesTheBoxWithWalls (1417 ms)
60: [----------] 3 tests from PmeTest (12286 ms total)
60:
60: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -4.79910463671071e+01
60: Maximum force = 1.86297359432220e+02 on atom 13
60: Norm of force = 8.77219865482161e+01
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
60:
60: Generated 330891 of the 330891 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (7127 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 3.02331e+02 on atom 3
60: F-Norm = 1.18024e+02
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -5.58622538633291e+01
60: Maximum force = 4.27274822366526e+02 on atom 13
60: Norm of force = 1.84530029253829e+02
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
60:
60: Generated 330891 of the 330891 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (8620 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 22.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 3.19376899751521e+02
60: Maximum force = 9.99884921009767e+03 on atom 9
60: Norm of force = 4.61669565054298e+03
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: turning H bonds into constraints...
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (4160 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60:
60: NOTE 3 [file glycine_vacuo.top, line 12]:
60: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
60:
60: Number of degrees of freedom in T-Coupling group System is 22.00
60:
60: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 4 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 2.41575e+04 on atom 10
60: F-Norm = 1.18451e+04
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 1.51743018140926e+02
60: Maximum force = 7.42089573409112e+03 on atom 9
60: Norm of force = 3.56929298615739e+03
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: turning H bonds into constraints...
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (5789 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60:
60: NOTE 3 [file unknown]:
60: You are using constraints on all bonds, whereas the forcefield has been
60: parametrized only with constraints involving hydrogen atoms. We suggest
60: using constraints = h-bonds instead, this will also improve performance.
60:
60: Number of degrees of freedom in T-Coupling group System is 23.00
60:
60: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 4 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -1.56984193848276e+02
60: Maximum force = 4.56923624626296e+02 on atom 17
60: Norm of force = 1.83258377168331e+02
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations
60:
60: Generated 2145 of the 2145 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
60:
60: turning all bonds into constraints...
60:
60: Cleaning up constraints and constant bonded interactions with virtual sites
60:
60: Removed 18 Angles with virtual sites, 21 left
60:
60: Removed 10 Proper Dih.s with virtual sites, 44 left
60:
60: Converted 15 Constraints with virtual sites to connections, 7 left
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (4785 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60:
60: NOTE 3 [file unknown]:
60: You are using constraints on all bonds, whereas the forcefield has been
60: parametrized only with constraints involving hydrogen atoms. We suggest
60: using constraints = h-bonds instead, this will also improve performance.
60:
60:
60: NOTE 4 [file unknown]:
60: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
60:
60: Number of degrees of freedom in T-Coupling group System is 23.00
60:
60: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 5 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 1.06800e+03 on atom 28
60: F-Norm = 4.26922e+02
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -1.69410778678185e+02
60: Maximum force = 2.18225948474048e+02 on atom 17
60: Norm of force = 7.92068036537643e+01
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations
60:
60: Generated 2145 of the 2145 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
60:
60: turning all bonds into constraints...
60:
60: Cleaning up constraints and constant bonded interactions with virtual sites
60:
60: Removed 18 Angles with virtual sites, 21 left
60:
60: Removed 10 Proper Dih.s with virtual sites, 44 left
60:
60: Converted 15 Constraints with virtual sites to connections, 7 left
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (7036 ms)
60: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (37518 ms total)
60:
60: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Number of degrees of freedom in T-Coupling group System is 33.00
60:
60: There were 2 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents converged to Fmax < 10 in 1 steps
60: Potential Energy = -9.74257075835450e-01
60: Maximum force = 4.01322929015108e+00 on atom 3
60: Norm of force = 1.63839399694368e+00
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
60:
60: Excluding 1 bonded neighbours molecule type 'Argon'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (1623 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Number of degrees of freedom in T-Coupling group System is 33.00
60:
60: There were 2 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 4.01323e+00 on atom 3
60: F-Norm = 1.63839e+00
60:
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
60: Potential Energy = -9.90642313893957e-01
60: Maximum force = 2.57812909491105e+00 on atom 3
60: Norm of force = 1.05251679559258e+00
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
60:
60: Excluding 1 bonded neighbours molecule type 'Argon'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (2128 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60:
60: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
60:
60: Number of degrees of freedom in T-Coupling group System is 33.00
60:
60: There were 2 notes
60:
60: There was 1 warning
60: Generated 1 of the 1 non-bonded parameter combinations
60:
60: Excluding 1 bonded neighbours molecule type 'Argon'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (22 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 3.19395484891518e+02
60: Maximum force = 9.97041707197910e+03 on atom 9
60: Norm of force = 4.62274878665467e+03
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (3888 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 2.41672e+04 on atom 10
60: F-Norm = 1.19357e+04
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 1.56258793899479e+02
60: Maximum force = 7.50181017480397e+03 on atom 9
60: Norm of force = 3.61390332564874e+03
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (5419 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60:
60: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60:
60: There was 1 warning
60: Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (1023 ms)
60: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (14105 ms total)
60:
60: [----------] Global test environment tear-down
60: [==========] 22 tests from 7 test cases ran. (72499 ms total)
60: [ PASSED ] 22 tests.
60:
60: YOU HAVE 4 DISABLED TESTS
60:
60/65 Test #60: MdrunMpiTests ......................... Passed 72.62 sec
test 61
Start 61: MdrunMpiPmeTests
61: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiPmeTests.xml"
61: Test timeout computed to be: 600
61: [==========] Running 3 tests from 1 test case.
61: [----------] Global test environment set-up.
61: [----------] 3 tests from PmeTest
61: [ RUN ] PmeTest.ReproducesEnergies
61: Number of degrees of freedom in T-Coupling group rest is 12.00
61:
61: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
61: NVE simulation: will use the initial temperature of 1046.791 K for
61: determining the Verlet buffer size
61:
61:
61: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
61: The optimal PME mesh load for parallel simulations is below 0.5
61: and for highly parallel simulations between 0.25 and 0.33,
61: for higher performance, increase the cut-off and the PME grid spacing.
61:
61:
61:
61: There were 2 notes
61: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 20 steps, 0.0 ps.
61: Setting the LD random seed to -268435713
61:
61: Generated 8 of the 10 non-bonded parameter combinations
61:
61: Excluding 2 bonded neighbours molecule type 'Methanol'
61:
61: Excluding 2 bonded neighbours molecule type 'SOL'
61:
61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
61:
61: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
61:
61: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
61:
61: Note that mdrun will redetermine rlist based on the actual pair-list setup
61: Calculating fourier grid dimensions for X Y Z
61: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
61:
61: Estimate for the relative computational load of the PME mesh part: 1.00
61:
61: This run will generate roughly 0 Mb of data
61:
61: Writing final coordinates.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 1.520 0.380 399.7
61: (ns/day) (hour/ns)
61: Performance: 4.772 5.029
61: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
61:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61:
61: Non-default thread affinity set, disabling internal thread affinity
61:
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 20 steps, 0.0 ps.
61:
61: Writing final coordinates.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 8.884 2.259 393.3
61: (ns/day) (hour/ns)
61: Performance: 0.803 29.884
61: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
61:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61:
61: Non-default thread affinity set, disabling internal thread affinity
61:
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61:
61: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
61: starting mdrun 'spc-and-methanol'
61: 20 steps, 0.0 ps.
61:
61: Writing final coordinates.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 9.165 2.330 393.4
61: (ns/day) (hour/ns)
61: Performance: 0.779 30.817
61: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
61:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (6963 ms)
61: [ RUN ] PmeTest.ScalesTheBox
61:
61: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
61: For a correct single-point energy evaluation with nsteps = 0, use
61: continuation = yes to avoid constraining the input coordinates.
61:
61: Number of degrees of freedom in T-Coupling group rest is 12.00
61:
61: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
61: NVE simulation: will use the initial temperature of 1046.791 K for
61: determining the Verlet buffer size
61:
61:
61: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
61: The optimal PME mesh load for parallel simulations is below 0.5
61: and for highly parallel simulations between 0.25 and 0.33,
61: for higher performance, increase the cut-off and the PME grid spacing.
61:
61:
61:
61: There were 3 notes
61: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61:
61: Non-default thread affinity set, disabling internal thread affinity
61:
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 0 steps, 0.0 ps.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.401 0.140 286.7
61: (ns/day) (hour/ns)
61: Performance: 0.618 38.834
61: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
61:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 1879044511
61:
61: Generated 8 of the 10 non-bonded parameter combinations
61:
61: Excluding 2 bonded neighbours molecule type 'Methanol'
61:
61: Excluding 2 bonded neighbours molecule type 'SOL'
61:
61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
61:
61: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
61:
61: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
61:
61: Note that mdrun will redetermine rlist based on the actual pair-list setup
61: Calculating fourier grid dimensions for X Y Z
61: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
61:
61: Estimate for the relative computational load of the PME mesh part: 1.00
61:
61: This run will generate roughly 0 Mb of data
61: [ OK ] PmeTest.ScalesTheBox (1097 ms)
61: [ RUN ] PmeTest.ScalesTheBoxWithWalls
61:
61: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
61: For a correct single-point energy evaluation with nsteps = 0, use
61: continuation = yes to avoid constraining the input coordinates.
61:
61: Number of degrees of freedom in T-Coupling group rest is 13.00
61:
61: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
61: NVE simulation: will use the initial temperature of 966.268 K for
61: determining the Verlet buffer size
61:
61:
61: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
61: The optimal PME mesh load for parallel simulations is below 0.5
61: and for highly parallel simulations between 0.25 and 0.33,
61: for higher performance, increase the cut-off and the PME grid spacing.
61:
61:
61:
61: There were 3 notes
61: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61:
61: Non-default thread affinity set, disabling internal thread affinity
61:
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 0 steps, 0.0 ps.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.861 0.255 337.8
61: (ns/day) (hour/ns)
61: Performance: 0.339 70.777
61: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
61:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -1155547282
61:
61: Generated 8 of the 10 non-bonded parameter combinations
61:
61: Excluding 2 bonded neighbours molecule type 'Methanol'
61:
61: Excluding 2 bonded neighbours molecule type 'SOL'
61:
61: Searching the wall atom type(s)
61:
61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
61:
61: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
61:
61: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
61:
61: Note that mdrun will redetermine rlist based on the actual pair-list setup
61: Calculating fourier grid dimensions for X Y Z
61: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
61:
61: Estimate for the relative computational load of the PME mesh part: 1.00
61:
61: This run will generate roughly 0 Mb of data
61: [ OK ] PmeTest.ScalesTheBoxWithWalls (1427 ms)
61: [----------] 3 tests from PmeTest (9487 ms total)
61:
61: [----------] Global test environment tear-down
61: [==========] 3 tests from 1 test case ran. (9527 ms total)
61: [ PASSED ] 3 tests.
61/65 Test #61: MdrunMpiPmeTests ...................... Passed 9.60 sec
test 62
Start 62: MdrunMpiCoordinationTestsOneRank
62: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml"
62: Test timeout computed to be: 1920
62: [==========] Running 39 tests from 3 test cases.
62: [----------] Global test environment set-up.
62: [----------] 1 test from BasicPropagators/PeriodicActionsTest
62: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.241 0.241 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.089 3.942
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.220 0.221 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.646 3.611
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.260 0.260 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.639 4.256
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.265 0.266 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.524 4.345
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.371 0.372 99.8
62: (ns/day) (hour/ns)
62: Performance: 3.949 6.078
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.334 0.334 99.8
62: (ns/day) (hour/ns)
62: Performance: 4.394 5.462
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1923 ms)
62: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1924 ms total)
62:
62: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.244 0.244 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.009 3.994
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.353 0.354 99.7
62: (ns/day) (hour/ns)
62: Performance: 4.155 5.777
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.256 0.257 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.721 4.195
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.271 0.272 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.408 4.438
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.215 0.216 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.807 3.526
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.232 0.232 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.320 3.797
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1895 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.223 0.224 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.571 3.652
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.242 0.243 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.054 3.964
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.294 0.295 99.8
62: (ns/day) (hour/ns)
62: Performance: 4.980 4.819
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.267 0.270 99.1
62: (ns/day) (hour/ns)
62: Performance: 5.441 4.411
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.278 0.279 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.266 4.557
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.354 0.354 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.149 5.785
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1898 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.295 0.296 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.968 4.831
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.257 0.258 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.700 4.210
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.243 0.244 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.031 3.979
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.267 0.267 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.496 4.367
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.290 0.290 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.057 4.745
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.250 0.251 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.863 4.093
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1895 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.263 0.263 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.588 4.295
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.277 0.278 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.292 4.535
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.241 0.242 99.5
62: (ns/day) (hour/ns)
62: Performance: 6.074 3.951
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.206 0.208 99.3
62: (ns/day) (hour/ns)
62: Performance: 7.070 3.394
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.238 0.239 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.143 3.907
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.256 0.256 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.732 4.187
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1708 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.210 0.210 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.993 3.432
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.224 0.224 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.553 3.662
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.304 0.305 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.819 4.980
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.237 0.237 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.195 3.874
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.247 0.247 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.937 4.043
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.319 0.319 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.602 5.215
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1769 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.711 0.711 99.9
62: (ns/day) (hour/ns)
62: Performance: 2.065 11.621
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.271 0.271 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.412 4.435
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.257 0.258 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.700 4.210
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.336 0.337 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.359 5.506
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.541 0.541 99.9
62: (ns/day) (hour/ns)
62: Performance: 2.713 8.845
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 1.245 1.246 100.0
62: (ns/day) (hour/ns)
62: Performance: 1.179 20.357
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (3795 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.678 0.678 100.0
62: (ns/day) (hour/ns)
62: Performance: 2.165 11.084
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.606 0.607 99.9
62: (ns/day) (hour/ns)
62: Performance: 2.420 9.917
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.224 0.226 99.3
62: (ns/day) (hour/ns)
62: Performance: 6.502 3.691
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.213 0.214 99.6
62: (ns/day) (hour/ns)
62: Performance: 6.875 3.491
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.224 0.227 99.1
62: (ns/day) (hour/ns)
62: Performance: 6.485 3.701
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.236 0.236 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.215 3.862
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (2473 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.255 0.255 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.755 4.170
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.236 0.237 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.203 3.869
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.318 0.319 99.8
62: (ns/day) (hour/ns)
62: Performance: 4.609 5.207
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.321 0.322 99.8
62: (ns/day) (hour/ns)
62: Performance: 4.563 5.259
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.271 0.272 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.402 4.443
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.287 0.288 99.5
62: (ns/day) (hour/ns)
62: Performance: 5.095 4.710
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1937 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.314 0.314 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.671 5.138
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.556 0.557 99.9
62: (ns/day) (hour/ns)
62: Performance: 2.637 9.101
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.414 0.415 99.9
62: (ns/day) (hour/ns)
62: Performance: 3.542 6.776
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.254 0.254 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.781 4.152
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.243 0.244 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.029 3.981
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.288 0.288 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.092 4.713
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (2285 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.280 0.280 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.245 4.576
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.291 0.292 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.036 4.766
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.241 0.241 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.091 3.940
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.264 0.265 99.4
62: (ns/day) (hour/ns)
62: Performance: 5.539 4.333
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.232 0.233 99.5
62: (ns/day) (hour/ns)
62: Performance: 6.295 3.813
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.268 0.268 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.478 4.381
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1835 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.249 0.249 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.896 4.070
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.257 0.257 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.707 4.205
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.243 0.243 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.043 3.971
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.268 0.268 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.479 4.380
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.265 0.266 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.529 4.341
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.253 0.253 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.794 4.142
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1754 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.250 0.250 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.866 4.092
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.218 0.219 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.712 3.575
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.246 0.247 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.952 4.032
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.216 0.216 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.787 3.536
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.184 0.185 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.956 3.017
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.184 0.185 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.957 3.016
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1546 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.202 0.202 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.261 3.305
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.232 0.232 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.320 3.798
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-4 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.239 0.240 99.6
62: (ns/day) (hour/ns)
62: Performance: 6.112 3.926
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>